Ben Bolstad
| Snapshot Date: 2024-08-25 14:00 -0400 (Sun, 25 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_19 |
| git_last_commit: af6c73d |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-08-27 17:41 -0400 (Tue, 27 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4523 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 249/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.68.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.68.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz |
| StartedAt: 2024-08-26 02:03:57 -0400 (Mon, 26 Aug 2024) |
| EndedAt: 2024-08-26 02:05:15 -0400 (Mon, 26 Aug 2024) |
| EllapsedTime: 78.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.68.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.594 0.200 0.836
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 474173 25.4 1035481 55.4 NA 638597 34.2
Vcells 877659 6.7 8388608 64.0 65536 2072435 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Aug 26 02:04:33 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Aug 26 02:04:33 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x600000d9c000>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Aug 26 02:04:40 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Aug 26 02:04:43 2024"
>
> ColMode(tmp2)
<pointer: 0x600000d9c000>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.3939308 0.5398050 0.5117220 -0.59262673
[2,] 0.8126314 -1.1288831 -0.3957404 0.06089165
[3,] 1.6070852 0.7977457 -0.9849103 1.70940252
[4,] 0.3130796 -0.9106585 -1.1383514 2.12601748
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.3939308 0.5398050 0.5117220 0.59262673
[2,] 0.8126314 1.1288831 0.3957404 0.06089165
[3,] 1.6070852 0.7977457 0.9849103 1.70940252
[4,] 0.3130796 0.9106585 1.1383514 2.12601748
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0196772 0.7347143 0.7153474 0.7698225
[2,] 0.9014607 1.0624891 0.6290790 0.2467623
[3,] 1.2677086 0.8931661 0.9924265 1.3074412
[4,] 0.5595352 0.9542843 1.0669355 1.4580869
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.59070 32.88695 32.66520 33.29085
[2,] 34.82724 36.75377 31.68653 27.52851
[3,] 39.28417 34.72941 35.90918 39.78381
[4,] 30.90843 35.45350 36.80771 41.70689
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600000da0000>
> exp(tmp5)
<pointer: 0x600000da0000>
> log(tmp5,2)
<pointer: 0x600000da0000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.5375
> Min(tmp5)
[1] 53.06951
> mean(tmp5)
[1] 72.28292
> Sum(tmp5)
[1] 14456.58
> Var(tmp5)
[1] 866.6762
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.71064 68.48283 74.28023 70.81124 71.22301 65.82333 69.93156 67.48851
[9] 74.66225 68.41563
> rowSums(tmp5)
[1] 1834.213 1369.657 1485.605 1416.225 1424.460 1316.467 1398.631 1349.770
[9] 1493.245 1368.313
> rowVars(tmp5)
[1] 7958.35533 57.86453 79.14605 71.68875 73.95346 71.56706
[7] 58.09221 72.51673 42.79722 75.50652
> rowSd(tmp5)
[1] 89.209615 7.606874 8.896407 8.466921 8.599620 8.459732 7.621825
[8] 8.515676 6.541958 8.689449
> rowMax(tmp5)
[1] 469.53749 82.40060 94.66616 86.80742 85.49890 82.54209 85.22276
[8] 81.89665 87.50303 86.10516
> rowMin(tmp5)
[1] 61.66823 54.65086 56.59323 54.13855 55.84388 54.80520 57.87395 53.06951
[9] 62.35391 54.08276
>
> colMeans(tmp5)
[1] 112.65325 68.21472 72.43076 67.38163 66.15711 66.15236 71.87791
[8] 74.32307 69.68843 72.50539 66.46858 71.77916 69.21331 73.48395
[15] 67.27266 72.50769 68.18728 75.19454 68.53638 71.63026
> colSums(tmp5)
[1] 1126.5325 682.1472 724.3076 673.8163 661.5711 661.5236 718.7791
[8] 743.2307 696.8843 725.0539 664.6858 717.7916 692.1331 734.8395
[15] 672.7266 725.0769 681.8728 751.9454 685.3638 716.3026
> colVars(tmp5)
[1] 15802.93782 49.76976 68.15761 121.87015 77.51618 41.26269
[7] 70.48778 88.25561 28.77961 57.32343 49.70830 57.89265
[13] 56.51720 59.88085 72.80348 32.33419 22.08342 150.05103
[19] 62.49465 119.30429
> colSd(tmp5)
[1] 125.709736 7.054769 8.255762 11.039481 8.804327 6.423604
[7] 8.395700 9.394445 5.364663 7.571224 7.050412 7.608722
[13] 7.517792 7.738272 8.532495 5.686316 4.699300 12.249532
[19] 7.905356 10.922650
> colMax(tmp5)
[1] 469.53749 76.49817 83.76648 86.80742 82.40060 76.52626 80.48611
[8] 83.88205 77.56745 81.89665 78.78279 80.02347 81.13245 82.74786
[15] 82.04983 78.73808 73.52649 94.66616 83.12467 87.50303
> colMin(tmp5)
[1] 54.14528 57.69325 60.79450 54.08276 55.84388 56.10558 54.13855 54.65086
[9] 62.04979 60.01975 53.06951 57.16404 58.72254 61.30065 57.87395 62.24219
[17] 58.45441 60.54903 57.93118 55.46708
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.71064 68.48283 NA 70.81124 71.22301 65.82333 69.93156 67.48851
[9] 74.66225 68.41563
> rowSums(tmp5)
[1] 1834.213 1369.657 NA 1416.225 1424.460 1316.467 1398.631 1349.770
[9] 1493.245 1368.313
> rowVars(tmp5)
[1] 7958.35533 57.86453 83.49461 71.68875 73.95346 71.56706
[7] 58.09221 72.51673 42.79722 75.50652
> rowSd(tmp5)
[1] 89.209615 7.606874 9.137538 8.466921 8.599620 8.459732 7.621825
[8] 8.515676 6.541958 8.689449
> rowMax(tmp5)
[1] 469.53749 82.40060 NA 86.80742 85.49890 82.54209 85.22276
[8] 81.89665 87.50303 86.10516
> rowMin(tmp5)
[1] 61.66823 54.65086 NA 54.13855 55.84388 54.80520 57.87395 53.06951
[9] 62.35391 54.08276
>
> colMeans(tmp5)
[1] 112.65325 68.21472 72.43076 67.38163 66.15711 66.15236 71.87791
[8] 74.32307 69.68843 72.50539 66.46858 NA 69.21331 73.48395
[15] 67.27266 72.50769 68.18728 75.19454 68.53638 71.63026
> colSums(tmp5)
[1] 1126.5325 682.1472 724.3076 673.8163 661.5711 661.5236 718.7791
[8] 743.2307 696.8843 725.0539 664.6858 NA 692.1331 734.8395
[15] 672.7266 725.0769 681.8728 751.9454 685.3638 716.3026
> colVars(tmp5)
[1] 15802.93782 49.76976 68.15761 121.87015 77.51618 41.26269
[7] 70.48778 88.25561 28.77961 57.32343 49.70830 NA
[13] 56.51720 59.88085 72.80348 32.33419 22.08342 150.05103
[19] 62.49465 119.30429
> colSd(tmp5)
[1] 125.709736 7.054769 8.255762 11.039481 8.804327 6.423604
[7] 8.395700 9.394445 5.364663 7.571224 7.050412 NA
[13] 7.517792 7.738272 8.532495 5.686316 4.699300 12.249532
[19] 7.905356 10.922650
> colMax(tmp5)
[1] 469.53749 76.49817 83.76648 86.80742 82.40060 76.52626 80.48611
[8] 83.88205 77.56745 81.89665 78.78279 NA 81.13245 82.74786
[15] 82.04983 78.73808 73.52649 94.66616 83.12467 87.50303
> colMin(tmp5)
[1] 54.14528 57.69325 60.79450 54.08276 55.84388 56.10558 54.13855 54.65086
[9] 62.04979 60.01975 53.06951 NA 58.72254 61.30065 57.87395 62.24219
[17] 58.45441 60.54903 57.93118 55.46708
>
> Max(tmp5,na.rm=TRUE)
[1] 469.5375
> Min(tmp5,na.rm=TRUE)
[1] 53.06951
> mean(tmp5,na.rm=TRUE)
[1] 72.26831
> Sum(tmp5,na.rm=TRUE)
[1] 14381.39
> Var(tmp5,na.rm=TRUE)
[1] 871.0104
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.71064 68.48283 74.23233 70.81124 71.22301 65.82333 69.93156 67.48851
[9] 74.66225 68.41563
> rowSums(tmp5,na.rm=TRUE)
[1] 1834.213 1369.657 1410.414 1416.225 1424.460 1316.467 1398.631 1349.770
[9] 1493.245 1368.313
> rowVars(tmp5,na.rm=TRUE)
[1] 7958.35533 57.86453 83.49461 71.68875 73.95346 71.56706
[7] 58.09221 72.51673 42.79722 75.50652
> rowSd(tmp5,na.rm=TRUE)
[1] 89.209615 7.606874 9.137538 8.466921 8.599620 8.459732 7.621825
[8] 8.515676 6.541958 8.689449
> rowMax(tmp5,na.rm=TRUE)
[1] 469.53749 82.40060 94.66616 86.80742 85.49890 82.54209 85.22276
[8] 81.89665 87.50303 86.10516
> rowMin(tmp5,na.rm=TRUE)
[1] 61.66823 54.65086 56.59323 54.13855 55.84388 54.80520 57.87395 53.06951
[9] 62.35391 54.08276
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.65325 68.21472 72.43076 67.38163 66.15711 66.15236 71.87791
[8] 74.32307 69.68843 72.50539 66.46858 71.40013 69.21331 73.48395
[15] 67.27266 72.50769 68.18728 75.19454 68.53638 71.63026
> colSums(tmp5,na.rm=TRUE)
[1] 1126.5325 682.1472 724.3076 673.8163 661.5711 661.5236 718.7791
[8] 743.2307 696.8843 725.0539 664.6858 642.6012 692.1331 734.8395
[15] 672.7266 725.0769 681.8728 751.9454 685.3638 716.3026
> colVars(tmp5,na.rm=TRUE)
[1] 15802.93782 49.76976 68.15761 121.87015 77.51618 41.26269
[7] 70.48778 88.25561 28.77961 57.32343 49.70830 63.51304
[13] 56.51720 59.88085 72.80348 32.33419 22.08342 150.05103
[19] 62.49465 119.30429
> colSd(tmp5,na.rm=TRUE)
[1] 125.709736 7.054769 8.255762 11.039481 8.804327 6.423604
[7] 8.395700 9.394445 5.364663 7.571224 7.050412 7.969507
[13] 7.517792 7.738272 8.532495 5.686316 4.699300 12.249532
[19] 7.905356 10.922650
> colMax(tmp5,na.rm=TRUE)
[1] 469.53749 76.49817 83.76648 86.80742 82.40060 76.52626 80.48611
[8] 83.88205 77.56745 81.89665 78.78279 80.02347 81.13245 82.74786
[15] 82.04983 78.73808 73.52649 94.66616 83.12467 87.50303
> colMin(tmp5,na.rm=TRUE)
[1] 54.14528 57.69325 60.79450 54.08276 55.84388 56.10558 54.13855 54.65086
[9] 62.04979 60.01975 53.06951 57.16404 58.72254 61.30065 57.87395 62.24219
[17] 58.45441 60.54903 57.93118 55.46708
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.71064 68.48283 NaN 70.81124 71.22301 65.82333 69.93156 67.48851
[9] 74.66225 68.41563
> rowSums(tmp5,na.rm=TRUE)
[1] 1834.213 1369.657 0.000 1416.225 1424.460 1316.467 1398.631 1349.770
[9] 1493.245 1368.313
> rowVars(tmp5,na.rm=TRUE)
[1] 7958.35533 57.86453 NA 71.68875 73.95346 71.56706
[7] 58.09221 72.51673 42.79722 75.50652
> rowSd(tmp5,na.rm=TRUE)
[1] 89.209615 7.606874 NA 8.466921 8.599620 8.459732 7.621825
[8] 8.515676 6.541958 8.689449
> rowMax(tmp5,na.rm=TRUE)
[1] 469.53749 82.40060 NA 86.80742 85.49890 82.54209 85.22276
[8] 81.89665 87.50303 86.10516
> rowMin(tmp5,na.rm=TRUE)
[1] 61.66823 54.65086 NA 54.13855 55.84388 54.80520 57.87395 53.06951
[9] 62.35391 54.08276
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.08530 67.76250 72.17415 65.66795 67.21977 65.54387 70.92145
[8] 74.77473 68.85297 73.89269 65.10034 NaN 70.14185 73.37871
[15] 65.63075 71.81543 67.96236 73.03103 67.63247 72.23157
> colSums(tmp5,na.rm=TRUE)
[1] 1044.7677 609.8625 649.5673 591.0115 604.9779 589.8948 638.2930
[8] 672.9726 619.6767 665.0342 585.9030 0.0000 631.2766 660.4084
[15] 590.6767 646.3388 611.6613 657.2792 608.6922 650.0841
> colVars(tmp5,na.rm=TRUE)
[1] 17645.79211 53.69032 75.93651 104.06586 74.50182 42.25502
[7] 69.00695 96.99255 24.52461 42.83728 34.86078 NA
[13] 53.88227 67.24136 51.57544 30.98461 24.27474 116.14852
[19] 61.11456 130.14964
> colSd(tmp5,na.rm=TRUE)
[1] 132.837465 7.327368 8.714156 10.201267 8.631444 6.500386
[7] 8.307042 9.848479 4.952233 6.545019 5.904302 NA
[13] 7.340454 8.200083 7.181605 5.566382 4.926940 10.777222
[19] 7.817580 11.408315
> colMax(tmp5,na.rm=TRUE)
[1] 469.53749 76.49817 83.76648 86.80742 82.40060 76.52626 78.28891
[8] 83.88205 77.56745 81.89665 71.90936 -Inf 81.13245 82.74786
[15] 79.51284 78.28581 73.52649 86.10516 83.12467 87.50303
> colMin(tmp5,na.rm=TRUE)
[1] 54.14528 57.69325 60.79450 54.08276 55.84388 56.10558 54.13855 54.65086
[9] 62.04979 65.67086 53.06951 Inf 58.72254 61.30065 57.87395 62.24219
[17] 58.45441 60.54903 57.93118 55.46708
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 401.0638 276.6407 148.9552 397.9358 240.3417 250.5654 151.8158 229.7032
[9] 186.2598 138.0567
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 401.0638 276.6407 148.9552 397.9358 240.3417 250.5654 151.8158 229.7032
[9] 186.2598 138.0567
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.842171e-14 1.421085e-13 0.000000e+00 -9.947598e-14 -1.136868e-13
[6] 1.705303e-13 3.552714e-14 0.000000e+00 -1.136868e-13 0.000000e+00
[11] 0.000000e+00 2.842171e-14 7.815970e-14 1.421085e-14 0.000000e+00
[16] 2.842171e-14 -2.273737e-13 2.842171e-14 8.526513e-14 -5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 12
8 3
3 18
7 6
6 7
5 17
4 12
6 5
3 3
1 10
2 16
5 9
10 9
9 20
3 13
4 5
1 1
9 4
8 10
9 12
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 3.169548
> Min(tmp)
[1] -3.084673
> mean(tmp)
[1] 0.09303707
> Sum(tmp)
[1] 9.303707
> Var(tmp)
[1] 1.160438
>
> rowMeans(tmp)
[1] 0.09303707
> rowSums(tmp)
[1] 9.303707
> rowVars(tmp)
[1] 1.160438
> rowSd(tmp)
[1] 1.077236
> rowMax(tmp)
[1] 3.169548
> rowMin(tmp)
[1] -3.084673
>
> colMeans(tmp)
[1] -1.848078651 1.925639593 0.365485114 0.028240299 1.816959319
[6] 0.054147347 1.114376442 1.814777947 1.019503456 0.532711013
[11] -0.735828490 3.169547987 -0.393088720 0.029858786 -1.360747049
[16] -0.410129199 -0.041606850 0.663046423 1.468702913 0.175259165
[21] 0.002541998 -0.705802597 1.141529054 1.471558473 0.379260805
[26] 0.138654900 -1.207739153 0.290027897 0.668646944 1.852540647
[31] -0.670222684 -0.867966555 2.068286630 0.491445367 0.782686933
[36] 0.164667711 -0.821750626 -1.503855581 0.455527164 -0.874304145
[41] -0.070662862 -0.089605613 -0.866131642 1.121640193 -0.212365502
[46] -1.381568386 -0.187009446 -0.265934980 -0.206489727 -1.041269443
[51] -0.903758439 -0.684574888 1.000840074 0.756837543 -1.036274320
[56] -1.028366386 -0.070460906 0.141552533 1.117197886 -0.324149181
[61] -0.220988535 -0.328147360 2.449224162 0.213239844 -0.334145998
[66] -1.599929472 0.360634349 -3.084673339 0.758441119 0.411278551
[71] 1.298639389 1.298661234 -0.333409065 -0.229319919 0.295947216
[76] -0.381932808 -1.683169351 0.061930896 -1.333270250 0.185993533
[81] 0.185759130 -0.513776129 0.654159963 1.315908730 -0.700046112
[86] 0.512204136 -1.306107840 -0.252487748 0.918920620 0.290981736
[91] 1.090529992 0.128278076 1.089984551 2.360475861 0.613149077
[96] -0.343822062 1.574179354 -0.715766600 -2.232361251 -1.585416958
> colSums(tmp)
[1] -1.848078651 1.925639593 0.365485114 0.028240299 1.816959319
[6] 0.054147347 1.114376442 1.814777947 1.019503456 0.532711013
[11] -0.735828490 3.169547987 -0.393088720 0.029858786 -1.360747049
[16] -0.410129199 -0.041606850 0.663046423 1.468702913 0.175259165
[21] 0.002541998 -0.705802597 1.141529054 1.471558473 0.379260805
[26] 0.138654900 -1.207739153 0.290027897 0.668646944 1.852540647
[31] -0.670222684 -0.867966555 2.068286630 0.491445367 0.782686933
[36] 0.164667711 -0.821750626 -1.503855581 0.455527164 -0.874304145
[41] -0.070662862 -0.089605613 -0.866131642 1.121640193 -0.212365502
[46] -1.381568386 -0.187009446 -0.265934980 -0.206489727 -1.041269443
[51] -0.903758439 -0.684574888 1.000840074 0.756837543 -1.036274320
[56] -1.028366386 -0.070460906 0.141552533 1.117197886 -0.324149181
[61] -0.220988535 -0.328147360 2.449224162 0.213239844 -0.334145998
[66] -1.599929472 0.360634349 -3.084673339 0.758441119 0.411278551
[71] 1.298639389 1.298661234 -0.333409065 -0.229319919 0.295947216
[76] -0.381932808 -1.683169351 0.061930896 -1.333270250 0.185993533
[81] 0.185759130 -0.513776129 0.654159963 1.315908730 -0.700046112
[86] 0.512204136 -1.306107840 -0.252487748 0.918920620 0.290981736
[91] 1.090529992 0.128278076 1.089984551 2.360475861 0.613149077
[96] -0.343822062 1.574179354 -0.715766600 -2.232361251 -1.585416958
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -1.848078651 1.925639593 0.365485114 0.028240299 1.816959319
[6] 0.054147347 1.114376442 1.814777947 1.019503456 0.532711013
[11] -0.735828490 3.169547987 -0.393088720 0.029858786 -1.360747049
[16] -0.410129199 -0.041606850 0.663046423 1.468702913 0.175259165
[21] 0.002541998 -0.705802597 1.141529054 1.471558473 0.379260805
[26] 0.138654900 -1.207739153 0.290027897 0.668646944 1.852540647
[31] -0.670222684 -0.867966555 2.068286630 0.491445367 0.782686933
[36] 0.164667711 -0.821750626 -1.503855581 0.455527164 -0.874304145
[41] -0.070662862 -0.089605613 -0.866131642 1.121640193 -0.212365502
[46] -1.381568386 -0.187009446 -0.265934980 -0.206489727 -1.041269443
[51] -0.903758439 -0.684574888 1.000840074 0.756837543 -1.036274320
[56] -1.028366386 -0.070460906 0.141552533 1.117197886 -0.324149181
[61] -0.220988535 -0.328147360 2.449224162 0.213239844 -0.334145998
[66] -1.599929472 0.360634349 -3.084673339 0.758441119 0.411278551
[71] 1.298639389 1.298661234 -0.333409065 -0.229319919 0.295947216
[76] -0.381932808 -1.683169351 0.061930896 -1.333270250 0.185993533
[81] 0.185759130 -0.513776129 0.654159963 1.315908730 -0.700046112
[86] 0.512204136 -1.306107840 -0.252487748 0.918920620 0.290981736
[91] 1.090529992 0.128278076 1.089984551 2.360475861 0.613149077
[96] -0.343822062 1.574179354 -0.715766600 -2.232361251 -1.585416958
> colMin(tmp)
[1] -1.848078651 1.925639593 0.365485114 0.028240299 1.816959319
[6] 0.054147347 1.114376442 1.814777947 1.019503456 0.532711013
[11] -0.735828490 3.169547987 -0.393088720 0.029858786 -1.360747049
[16] -0.410129199 -0.041606850 0.663046423 1.468702913 0.175259165
[21] 0.002541998 -0.705802597 1.141529054 1.471558473 0.379260805
[26] 0.138654900 -1.207739153 0.290027897 0.668646944 1.852540647
[31] -0.670222684 -0.867966555 2.068286630 0.491445367 0.782686933
[36] 0.164667711 -0.821750626 -1.503855581 0.455527164 -0.874304145
[41] -0.070662862 -0.089605613 -0.866131642 1.121640193 -0.212365502
[46] -1.381568386 -0.187009446 -0.265934980 -0.206489727 -1.041269443
[51] -0.903758439 -0.684574888 1.000840074 0.756837543 -1.036274320
[56] -1.028366386 -0.070460906 0.141552533 1.117197886 -0.324149181
[61] -0.220988535 -0.328147360 2.449224162 0.213239844 -0.334145998
[66] -1.599929472 0.360634349 -3.084673339 0.758441119 0.411278551
[71] 1.298639389 1.298661234 -0.333409065 -0.229319919 0.295947216
[76] -0.381932808 -1.683169351 0.061930896 -1.333270250 0.185993533
[81] 0.185759130 -0.513776129 0.654159963 1.315908730 -0.700046112
[86] 0.512204136 -1.306107840 -0.252487748 0.918920620 0.290981736
[91] 1.090529992 0.128278076 1.089984551 2.360475861 0.613149077
[96] -0.343822062 1.574179354 -0.715766600 -2.232361251 -1.585416958
> colMedians(tmp)
[1] -1.848078651 1.925639593 0.365485114 0.028240299 1.816959319
[6] 0.054147347 1.114376442 1.814777947 1.019503456 0.532711013
[11] -0.735828490 3.169547987 -0.393088720 0.029858786 -1.360747049
[16] -0.410129199 -0.041606850 0.663046423 1.468702913 0.175259165
[21] 0.002541998 -0.705802597 1.141529054 1.471558473 0.379260805
[26] 0.138654900 -1.207739153 0.290027897 0.668646944 1.852540647
[31] -0.670222684 -0.867966555 2.068286630 0.491445367 0.782686933
[36] 0.164667711 -0.821750626 -1.503855581 0.455527164 -0.874304145
[41] -0.070662862 -0.089605613 -0.866131642 1.121640193 -0.212365502
[46] -1.381568386 -0.187009446 -0.265934980 -0.206489727 -1.041269443
[51] -0.903758439 -0.684574888 1.000840074 0.756837543 -1.036274320
[56] -1.028366386 -0.070460906 0.141552533 1.117197886 -0.324149181
[61] -0.220988535 -0.328147360 2.449224162 0.213239844 -0.334145998
[66] -1.599929472 0.360634349 -3.084673339 0.758441119 0.411278551
[71] 1.298639389 1.298661234 -0.333409065 -0.229319919 0.295947216
[76] -0.381932808 -1.683169351 0.061930896 -1.333270250 0.185993533
[81] 0.185759130 -0.513776129 0.654159963 1.315908730 -0.700046112
[86] 0.512204136 -1.306107840 -0.252487748 0.918920620 0.290981736
[91] 1.090529992 0.128278076 1.089984551 2.360475861 0.613149077
[96] -0.343822062 1.574179354 -0.715766600 -2.232361251 -1.585416958
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.848079 1.92564 0.3654851 0.0282403 1.816959 0.05414735 1.114376
[2,] -1.848079 1.92564 0.3654851 0.0282403 1.816959 0.05414735 1.114376
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.814778 1.019503 0.532711 -0.7358285 3.169548 -0.3930887 0.02985879
[2,] 1.814778 1.019503 0.532711 -0.7358285 3.169548 -0.3930887 0.02985879
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.360747 -0.4101292 -0.04160685 0.6630464 1.468703 0.1752592 0.002541998
[2,] -1.360747 -0.4101292 -0.04160685 0.6630464 1.468703 0.1752592 0.002541998
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.7058026 1.141529 1.471558 0.3792608 0.1386549 -1.207739 0.2900279
[2,] -0.7058026 1.141529 1.471558 0.3792608 0.1386549 -1.207739 0.2900279
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.6686469 1.852541 -0.6702227 -0.8679666 2.068287 0.4914454 0.7826869
[2,] 0.6686469 1.852541 -0.6702227 -0.8679666 2.068287 0.4914454 0.7826869
[,36] [,37] [,38] [,39] [,40] [,41]
[1,] 0.1646677 -0.8217506 -1.503856 0.4555272 -0.8743041 -0.07066286
[2,] 0.1646677 -0.8217506 -1.503856 0.4555272 -0.8743041 -0.07066286
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] -0.08960561 -0.8661316 1.12164 -0.2123655 -1.381568 -0.1870094 -0.265935
[2,] -0.08960561 -0.8661316 1.12164 -0.2123655 -1.381568 -0.1870094 -0.265935
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] -0.2064897 -1.041269 -0.9037584 -0.6845749 1.00084 0.7568375 -1.036274
[2,] -0.2064897 -1.041269 -0.9037584 -0.6845749 1.00084 0.7568375 -1.036274
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -1.028366 -0.07046091 0.1415525 1.117198 -0.3241492 -0.2209885 -0.3281474
[2,] -1.028366 -0.07046091 0.1415525 1.117198 -0.3241492 -0.2209885 -0.3281474
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] 2.449224 0.2132398 -0.334146 -1.599929 0.3606343 -3.084673 0.7584411
[2,] 2.449224 0.2132398 -0.334146 -1.599929 0.3606343 -3.084673 0.7584411
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] 0.4112786 1.298639 1.298661 -0.3334091 -0.2293199 0.2959472 -0.3819328
[2,] 0.4112786 1.298639 1.298661 -0.3334091 -0.2293199 0.2959472 -0.3819328
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -1.683169 0.0619309 -1.33327 0.1859935 0.1857591 -0.5137761 0.65416
[2,] -1.683169 0.0619309 -1.33327 0.1859935 0.1857591 -0.5137761 0.65416
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] 1.315909 -0.7000461 0.5122041 -1.306108 -0.2524877 0.9189206 0.2909817
[2,] 1.315909 -0.7000461 0.5122041 -1.306108 -0.2524877 0.9189206 0.2909817
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 1.09053 0.1282781 1.089985 2.360476 0.6131491 -0.3438221 1.574179
[2,] 1.09053 0.1282781 1.089985 2.360476 0.6131491 -0.3438221 1.574179
[,98] [,99] [,100]
[1,] -0.7157666 -2.232361 -1.585417
[2,] -0.7157666 -2.232361 -1.585417
>
>
> Max(tmp2)
[1] 2.529321
> Min(tmp2)
[1] -2.138931
> mean(tmp2)
[1] -0.0210775
> Sum(tmp2)
[1] -2.10775
> Var(tmp2)
[1] 0.9090968
>
> rowMeans(tmp2)
[1] 1.61106645 0.08201374 1.83936915 0.15651268 -0.55075119 -1.38229100
[7] 0.16876823 -0.27151486 -0.62210195 1.13423783 -0.33336121 -0.33714122
[13] -0.49418683 -0.70192341 1.61948253 -0.47281307 -1.13590431 -1.61099325
[19] 1.25273349 -0.13301455 -0.30996425 -0.24542441 -0.25324886 0.15468008
[25] 0.85458943 1.35283648 1.40172541 -0.85519795 -0.20145684 0.51301327
[31] -1.89452685 1.04158704 -0.29082436 0.38131172 -1.12395748 0.92425996
[37] -0.54289228 1.09373659 0.37218682 0.19203683 0.16014414 0.85403586
[43] -0.89152067 -2.07690135 0.26032264 0.49343985 0.21311291 0.16310400
[49] 0.12195736 -0.37823009 0.39871312 0.76269231 -0.49346237 -1.77720744
[55] -1.21575728 1.12382760 1.05854073 -1.13188593 0.70647458 -0.74645954
[61] -0.96774626 0.91621972 -0.58839830 0.48696752 -2.13893119 -0.84102946
[67] -0.04923668 -1.60272078 0.52862303 -0.41983111 -0.35099104 -1.45271883
[73] -0.78596865 0.15688944 0.44682877 1.12681029 0.93851293 0.25182091
[79] -0.72680427 1.11135296 0.56101937 -1.79723067 -0.83281106 0.49349560
[85] 0.25623744 0.16921967 0.01553081 1.04272680 1.11233004 -0.03930374
[91] 0.44855694 -0.17268804 -0.26140144 -0.60261480 0.90271272 1.29152429
[97] -2.04764399 -1.07159133 2.52932080 -0.13238652
> rowSums(tmp2)
[1] 1.61106645 0.08201374 1.83936915 0.15651268 -0.55075119 -1.38229100
[7] 0.16876823 -0.27151486 -0.62210195 1.13423783 -0.33336121 -0.33714122
[13] -0.49418683 -0.70192341 1.61948253 -0.47281307 -1.13590431 -1.61099325
[19] 1.25273349 -0.13301455 -0.30996425 -0.24542441 -0.25324886 0.15468008
[25] 0.85458943 1.35283648 1.40172541 -0.85519795 -0.20145684 0.51301327
[31] -1.89452685 1.04158704 -0.29082436 0.38131172 -1.12395748 0.92425996
[37] -0.54289228 1.09373659 0.37218682 0.19203683 0.16014414 0.85403586
[43] -0.89152067 -2.07690135 0.26032264 0.49343985 0.21311291 0.16310400
[49] 0.12195736 -0.37823009 0.39871312 0.76269231 -0.49346237 -1.77720744
[55] -1.21575728 1.12382760 1.05854073 -1.13188593 0.70647458 -0.74645954
[61] -0.96774626 0.91621972 -0.58839830 0.48696752 -2.13893119 -0.84102946
[67] -0.04923668 -1.60272078 0.52862303 -0.41983111 -0.35099104 -1.45271883
[73] -0.78596865 0.15688944 0.44682877 1.12681029 0.93851293 0.25182091
[79] -0.72680427 1.11135296 0.56101937 -1.79723067 -0.83281106 0.49349560
[85] 0.25623744 0.16921967 0.01553081 1.04272680 1.11233004 -0.03930374
[91] 0.44855694 -0.17268804 -0.26140144 -0.60261480 0.90271272 1.29152429
[97] -2.04764399 -1.07159133 2.52932080 -0.13238652
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 1.61106645 0.08201374 1.83936915 0.15651268 -0.55075119 -1.38229100
[7] 0.16876823 -0.27151486 -0.62210195 1.13423783 -0.33336121 -0.33714122
[13] -0.49418683 -0.70192341 1.61948253 -0.47281307 -1.13590431 -1.61099325
[19] 1.25273349 -0.13301455 -0.30996425 -0.24542441 -0.25324886 0.15468008
[25] 0.85458943 1.35283648 1.40172541 -0.85519795 -0.20145684 0.51301327
[31] -1.89452685 1.04158704 -0.29082436 0.38131172 -1.12395748 0.92425996
[37] -0.54289228 1.09373659 0.37218682 0.19203683 0.16014414 0.85403586
[43] -0.89152067 -2.07690135 0.26032264 0.49343985 0.21311291 0.16310400
[49] 0.12195736 -0.37823009 0.39871312 0.76269231 -0.49346237 -1.77720744
[55] -1.21575728 1.12382760 1.05854073 -1.13188593 0.70647458 -0.74645954
[61] -0.96774626 0.91621972 -0.58839830 0.48696752 -2.13893119 -0.84102946
[67] -0.04923668 -1.60272078 0.52862303 -0.41983111 -0.35099104 -1.45271883
[73] -0.78596865 0.15688944 0.44682877 1.12681029 0.93851293 0.25182091
[79] -0.72680427 1.11135296 0.56101937 -1.79723067 -0.83281106 0.49349560
[85] 0.25623744 0.16921967 0.01553081 1.04272680 1.11233004 -0.03930374
[91] 0.44855694 -0.17268804 -0.26140144 -0.60261480 0.90271272 1.29152429
[97] -2.04764399 -1.07159133 2.52932080 -0.13238652
> rowMin(tmp2)
[1] 1.61106645 0.08201374 1.83936915 0.15651268 -0.55075119 -1.38229100
[7] 0.16876823 -0.27151486 -0.62210195 1.13423783 -0.33336121 -0.33714122
[13] -0.49418683 -0.70192341 1.61948253 -0.47281307 -1.13590431 -1.61099325
[19] 1.25273349 -0.13301455 -0.30996425 -0.24542441 -0.25324886 0.15468008
[25] 0.85458943 1.35283648 1.40172541 -0.85519795 -0.20145684 0.51301327
[31] -1.89452685 1.04158704 -0.29082436 0.38131172 -1.12395748 0.92425996
[37] -0.54289228 1.09373659 0.37218682 0.19203683 0.16014414 0.85403586
[43] -0.89152067 -2.07690135 0.26032264 0.49343985 0.21311291 0.16310400
[49] 0.12195736 -0.37823009 0.39871312 0.76269231 -0.49346237 -1.77720744
[55] -1.21575728 1.12382760 1.05854073 -1.13188593 0.70647458 -0.74645954
[61] -0.96774626 0.91621972 -0.58839830 0.48696752 -2.13893119 -0.84102946
[67] -0.04923668 -1.60272078 0.52862303 -0.41983111 -0.35099104 -1.45271883
[73] -0.78596865 0.15688944 0.44682877 1.12681029 0.93851293 0.25182091
[79] -0.72680427 1.11135296 0.56101937 -1.79723067 -0.83281106 0.49349560
[85] 0.25623744 0.16921967 0.01553081 1.04272680 1.11233004 -0.03930374
[91] 0.44855694 -0.17268804 -0.26140144 -0.60261480 0.90271272 1.29152429
[97] -2.04764399 -1.07159133 2.52932080 -0.13238652
>
> colMeans(tmp2)
[1] -0.0210775
> colSums(tmp2)
[1] -2.10775
> colVars(tmp2)
[1] 0.9090968
> colSd(tmp2)
[1] 0.9534657
> colMax(tmp2)
[1] 2.529321
> colMin(tmp2)
[1] -2.138931
> colMedians(tmp2)
[1] 0.04877227
> colRanges(tmp2)
[,1]
[1,] -2.138931
[2,] 2.529321
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.9455790 1.4839647 0.7162174 0.9885919 -4.3315194 1.6929997
[7] 0.2615959 2.5947482 -1.0600479 -1.1062079
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.1661813
[2,] -0.9918601
[3,] -0.3811502
[4,] 0.1994804
[5,] 1.0105867
>
> rowApply(tmp,sum)
[1] 1.4173141 -1.6689050 -1.6525521 -2.0769788 2.0940419 -3.4731454
[7] 2.7830666 -2.1413279 0.5072372 1.5060130
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 1 3 9 2 7 2 1 9 1
[2,] 5 8 10 2 1 10 4 8 7 6
[3,] 8 7 6 8 10 2 10 7 4 3
[4,] 9 9 5 5 3 8 9 3 1 7
[5,] 6 3 4 1 8 3 1 10 10 4
[6,] 4 6 9 6 7 1 6 9 2 9
[7,] 10 2 7 4 5 5 3 5 6 5
[8,] 3 4 8 7 9 9 5 2 8 2
[9,] 1 10 1 3 4 6 8 4 5 10
[10,] 2 5 2 10 6 4 7 6 3 8
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.37332734 -2.46961249 -0.04704244 1.23665269 1.65278050 -0.17036674
[7] 4.62750858 -2.76813821 0.55399021 -2.64608547 1.64708841 -0.01174675
[13] -0.87271967 0.04650181 -2.96202672 4.71600630 -3.12720596 -0.01379050
[19] 2.90332436 0.73378814
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.26925855
[2,] -0.18759120
[3,] 0.06443097
[4,] 0.27214246
[5,] 2.49360366
>
> rowApply(tmp,sum)
[1] -0.03182818 12.05031073 -1.83526004 -9.46273296 4.68174386
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 20 7 13 9
[2,] 5 7 5 10 4
[3,] 4 12 19 12 5
[4,] 17 2 13 19 7
[5,] 12 19 2 14 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.06443097 -0.67987902 -0.7473626 0.5945359 0.06009059 0.03804106
[2,] 2.49360366 0.03466691 0.9213759 -1.3324723 2.38508494 -0.13116712
[3,] -0.26925855 -0.68205816 0.6186435 0.3574863 -1.78715472 -1.78923500
[4,] -0.18759120 -0.62483108 -0.3862350 1.5022325 -0.17524165 0.83593185
[5,] 0.27214246 -0.51751114 -0.4534642 0.1148703 1.17000135 0.87606249
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 2.2253959 -0.48524474 -0.2782792 -0.5108138 0.1576163 -0.5934026
[2,] 1.8102496 -2.07034942 0.7344928 -0.4218325 0.9927943 0.9716700
[3,] 0.2148893 -0.77033083 0.5884457 0.2188161 0.4041431 -0.3793669
[4,] -0.5848390 0.09803613 -0.9267136 -1.5343864 -1.1394637 -0.6963933
[5,] 0.9618127 0.45975064 0.4360445 -0.3978688 1.2319983 0.6857460
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.5855671 0.3476929 0.3836143 1.85195891 -1.5510636 -1.0491393
[2,] 0.7701234 1.6264045 -0.2548032 0.01721936 0.9807156 0.6740844
[3,] 0.1774687 -0.1879675 0.5115846 0.41938719 0.4625671 -0.8224457
[4,] -0.6505099 -2.3257674 -2.2683410 2.13039497 -1.6026151 0.3286621
[5,] -0.5842348 0.5861393 -1.3340813 0.29704587 -1.4168100 0.8550480
[,19] [,20]
[1,] 1.6838196 -0.9582726
[2,] 0.3989994 1.4494504
[3,] 0.7268100 0.1523157
[4,] -1.1457549 -0.1093073
[5,] 1.2394503 0.1996019
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 655 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 567 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -1.177793 0.7255536 -0.9056921 -0.4605556 -0.9948057 1.938776 -0.2094321
col8 col9 col10 col11 col12 col13 col14
row1 1.748451 0.6782814 0.8009946 0.5525103 0.7569184 1.113754 0.01731634
col15 col16 col17 col18 col19 col20
row1 0.159978 -0.06717732 -0.0856727 -0.001365062 1.101867 -0.2273223
> tmp[,"col10"]
col10
row1 0.8009946
row2 0.1402188
row3 0.5704844
row4 -0.7754522
row5 -1.4445681
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -1.177793 0.7255536 -0.9056921 -0.4605556 -0.9948057 1.938776 -0.20943210
row5 -1.068845 0.7790148 0.3328530 -0.4340872 -0.5435387 -1.279072 -0.04237188
col8 col9 col10 col11 col12 col13 col14
row1 1.74845103 0.6782814 0.8009946 0.5525103 0.7569184 1.113754 0.01731634
row5 0.08411142 1.3154439 -1.4445681 0.8882118 0.4827897 -1.929046 -0.20857459
col15 col16 col17 col18 col19 col20
row1 0.1599780 -0.06717732 -0.0856727 -0.001365062 1.1018670 -0.22732226
row5 0.8580761 0.83793379 -1.3929155 -1.639480306 -0.3567002 -0.07194472
> tmp[,c("col6","col20")]
col6 col20
row1 1.9387759 -0.22732226
row2 -1.0602542 0.66014492
row3 -0.5468835 -2.05963188
row4 -0.9942555 1.72033228
row5 -1.2790719 -0.07194472
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.938776 -0.22732226
row5 -1.279072 -0.07194472
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.16187 51.74759 50.21938 49.83906 50.00758 105.6237 48.57392 51.76209
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.3806 50.45908 50.25974 47.70928 47.52401 51.02408 49.61762 50.0176
col17 col18 col19 col20
row1 50.91579 51.37429 50.32947 105.1355
> tmp[,"col10"]
col10
row1 50.45908
row2 29.69002
row3 28.62808
row4 28.54947
row5 50.20824
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.16187 51.74759 50.21938 49.83906 50.00758 105.6237 48.57392 51.76209
row5 50.08602 49.59181 50.82933 50.50354 48.86295 106.6066 48.37850 49.66777
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.38060 50.45908 50.25974 47.70928 47.52401 51.02408 49.61762 50.01760
row5 49.97916 50.20824 49.30928 52.92932 49.38680 50.40074 48.90835 48.87156
col17 col18 col19 col20
row1 50.91579 51.37429 50.32947 105.1355
row5 50.83804 48.90411 49.63455 104.5458
> tmp[,c("col6","col20")]
col6 col20
row1 105.62366 105.13547
row2 75.65610 75.38047
row3 75.67419 73.20341
row4 74.72491 74.15429
row5 106.60657 104.54582
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.6237 105.1355
row5 106.6066 104.5458
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.6237 105.1355
row5 106.6066 104.5458
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.0424881
[2,] -2.3740512
[3,] -0.3689634
[4,] -1.0091558
[5,] -0.1528891
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.7053492 0.4291199
[2,] 1.0321341 0.2072656
[3,] 0.2771007 0.9821544
[4,] 0.3433501 -0.1685674
[5,] 0.9682324 -0.7114246
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.6444752 0.62354926
[2,] 1.1977781 0.39968256
[3,] -0.5556890 0.88460064
[4,] -0.8236127 -0.87314615
[5,] 1.4988650 0.05528781
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.6444752
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.6444752
[2,] 1.1977781
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 0.8155163 -0.7735546 0.6081178 -0.1654713 -0.2975431 0.09654191
row1 1.5427922 0.4669536 -0.3020188 -0.6728060 -0.6398801 0.94113185
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 0.2818418 -1.345710 0.4299341 -0.6580584 -1.575617 -1.9086222 1.967810
row1 -1.2865026 1.688108 -0.8688444 0.8833943 -1.664721 0.4947257 -1.129836
[,14] [,15] [,16] [,17] [,18] [,19]
row3 0.09016903 -1.301805 0.31682352 0.5537997 -0.6150731 -0.9795567
row1 -1.15566331 1.043641 0.02175885 0.9422628 0.9749574 0.6347756
[,20]
row3 -0.7887893
row1 0.3519815
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.01484328 3.401576 -0.5545007 0.2556923 0.188431 -0.9670656 1.14171
[,8] [,9] [,10]
row2 -1.550901 -0.7179462 -0.6047389
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.8860253 -0.5931531 0.6226223 0.8125736 1.247859 0.6992315 1.652529
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.03024819 0.2078683 1.274999 0.2682285 0.7124869 1.669559 0.5382538
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.1084838 -0.474295 0.3220688 -0.6039796 0.001323432 0.4787046
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x600000dbc0c0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc47b1552a"
[2] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc4b4e5d2b"
[3] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc5c6d8ad"
[4] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc41bb48d1"
[5] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc6ea9b30d"
[6] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc472a533d"
[7] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc2bbeee4b"
[8] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc40e945d"
[9] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc592e67bf"
[10] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc759d5a56"
[11] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc2d96006d"
[12] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc52f60b7c"
[13] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc176c2471"
[14] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc3ccc82ba"
[15] "/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM142bc169aa085"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x600000db8240>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600000db8240>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600000db8240>
> rowMedians(tmp)
[1] -0.337657534 -0.662226538 0.387437151 -0.028032013 -0.268866255
[6] -0.123701826 0.048050534 -0.095025933 -0.540685237 0.694299107
[11] 0.021515587 0.296947607 0.132741385 0.011980115 -0.683866718
[16] -0.097812705 -0.158209622 0.333801696 -0.161946140 -0.104198746
[21] -0.294491705 -0.325487727 0.335624816 0.041748901 -0.073308143
[26] -0.154983331 -0.766979375 -0.037551425 0.179192771 -0.112091984
[31] 0.681900751 0.031330481 0.103949638 0.243784140 0.501923237
[36] -0.430320585 -0.098953337 -0.238622847 0.278645389 0.296023028
[41] -0.156203198 0.169369636 0.102293985 0.103588759 -0.156395228
[46] -0.718528271 0.270173703 0.179371712 -0.183877904 0.038487469
[51] -0.243684245 0.059642212 0.177087469 0.138098552 0.018344824
[56] 0.736322898 0.347754668 0.042579576 -0.472034121 0.044752189
[61] 0.105539438 -0.713371122 -0.894760997 -0.119120140 0.552668376
[66] 0.108166294 0.321523569 0.188614315 0.111280634 -0.298483765
[71] 0.449096408 -0.379615393 -0.092927283 0.158091202 -0.343313890
[76] -0.282912429 -0.312597886 0.442499205 -0.058409627 -0.756613781
[81] -0.817072610 0.668820765 0.176148189 0.082046342 -0.193710300
[86] 0.152510806 0.143088720 -0.729691221 0.132258653 0.084095918
[91] 0.037483165 -0.223170979 -0.062166686 0.161151982 0.163336693
[96] -0.169568134 -0.644314852 -0.346285777 -0.219409706 -0.013345759
[101] -0.460534086 -0.190732670 0.078600188 0.202434846 0.115463672
[106] 0.325308202 -0.366628846 0.039870538 0.010033447 0.171086295
[111] -0.020676051 -0.397178307 -0.097018125 0.008111762 0.461203518
[116] 0.023798525 0.423085233 0.352404749 0.141039313 0.184051338
[121] -0.453387910 -0.295934458 0.004429203 0.008412787 -0.193116472
[126] -0.046438741 -0.127004764 -0.338094734 0.088704678 -0.007925083
[131] -0.060389342 0.153445303 0.190180363 -0.484711163 -0.248578508
[136] -0.301244982 0.459138979 -0.273855990 0.432366407 -0.134480043
[141] 0.052385544 -0.107067215 0.066065723 -0.443477624 -0.263955337
[146] 0.359480212 0.338913472 -0.078334982 -0.485943617 -0.099722789
[151] -0.623801656 0.060404552 -0.139564604 -0.189282313 0.128612737
[156] -0.369361595 0.278931683 -0.698754503 -0.365544284 0.163134606
[161] 0.078960838 -0.207943244 0.421890077 0.125584008 0.600103131
[166] -0.296310736 -0.159377133 0.038216998 0.158681474 -0.281507338
[171] -0.324512821 0.638057640 0.233277276 0.112551682 0.012508827
[176] 0.504787352 -0.640755137 -0.028209027 0.577171070 0.008597781
[181] 0.142411578 -0.375894320 0.011158271 0.191826385 0.001280724
[186] 0.378959197 0.406654253 -0.168591843 -0.372553817 -0.039326989
[191] -0.360454453 0.254660501 -0.135699776 -0.098421037 0.378456398
[196] 0.214664265 -0.199531879 -0.148555124 0.265553147 -0.167456709
[201] 0.074901434 0.269623367 0.113750264 -0.115421052 -0.313241005
[206] 0.122444770 -0.099685335 0.514098788 0.244566254 0.135871194
[211] -0.515533999 -0.117665403 0.334488156 -0.295696206 0.563426329
[216] 0.404903771 0.397717707 -0.014488234 -0.406529305 -0.243817668
[221] 0.055617622 0.541402369 0.178325466 0.014710773 0.844239751
[226] 0.358750331 0.533064345 -0.018268385 -0.315942012 -0.516542455
>
> proc.time()
user system elapsed
5.162 17.671 28.621
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000301c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000301c000>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000301c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x60000301c000>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x600003014000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003014000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x600003014000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003014000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003014000>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003010420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003010420>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003010420>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003010420>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003010420>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003010420>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003010420>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003010420>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003010420>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003008060>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003008060>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003008060>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003008060>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile16c9f2f8dbfb9" "BufferedMatrixFile16c9f3262313"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile16c9f2f8dbfb9" "BufferedMatrixFile16c9f3262313"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003008300>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003008300>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003008300>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003008300>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003008300>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003008300>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000300c000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000300c000>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60000300c000>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x60000300c000>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000301c3c0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000301c3c0>
> rm(P)
>
> proc.time()
user system elapsed
0.606 0.213 0.868
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.588 0.134 0.744