Ben Bolstad
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BufferedMatrix_1.68.0.tar.gz |
| StartedAt: 2024-06-12 21:12:16 -0400 (Wed, 12 Jun 2024) |
| EndedAt: 2024-06-12 21:12:40 -0400 (Wed, 12 Jun 2024) |
| EllapsedTime: 24.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BufferedMatrix_1.68.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init_package.c -o init_package.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.242 0.066 0.298
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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] "/home/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) max used (Mb)
Ncells 471778 25.2 1026221 54.9 643431 34.4
Vcells 871899 6.7 8388608 64.0 2046580 15.7
>
>
>
>
> ##
> ## 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] "Wed Jun 12 21:12:31 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] "Wed Jun 12 21:12:31 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: 0x56264d086a40>
>
>
>
> 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] "Wed Jun 12 21:12:32 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] "Wed Jun 12 21:12:32 2024"
>
> ColMode(tmp2)
<pointer: 0x56264d086a40>
>
>
>
> ### 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,] 100.2111151 1.11907516 -0.9368379 -1.6312027
[2,] -0.9597061 0.92293032 1.5068458 -0.2718627
[3,] -1.4400319 0.09562305 -0.3621720 -0.9644112
[4,] -1.9391258 -0.66250934 0.4160625 1.4358107
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 100.2111151 1.11907516 0.9368379 1.6312027
[2,] 0.9597061 0.92293032 1.5068458 0.2718627
[3,] 1.4400319 0.09562305 0.3621720 0.9644112
[4,] 1.9391258 0.66250934 0.4160625 1.4358107
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 10.0105502 1.0578635 0.9679038 1.2771854
[2,] 0.9796459 0.9606926 1.2275365 0.5214045
[3,] 1.2000133 0.3092298 0.6018073 0.9820444
[4,] 1.3925250 0.8139468 0.6450291 1.1982532
>
> 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: /home/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,] 225.31662 36.69771 35.61588 39.40306
[2,] 35.75616 35.52986 38.78221 30.48591
[3,] 38.44016 28.18792 31.38025 35.78486
[4,] 40.86438 33.80198 31.86635 38.41834
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x56264d65ecc0>
> exp(tmp5)
<pointer: 0x56264d65ecc0>
> log(tmp5,2)
<pointer: 0x56264d65ecc0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.967
> Min(tmp5)
[1] 52.33427
> mean(tmp5)
[1] 73.66143
> Sum(tmp5)
[1] 14732.29
> Var(tmp5)
[1] 870.1441
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.74088 70.88431 70.55779 74.36236 70.72620 73.08544 67.99556 72.75139
[9] 71.46641 72.04396
> rowSums(tmp5)
[1] 1854.818 1417.686 1411.156 1487.247 1414.524 1461.709 1359.911 1455.028
[9] 1429.328 1440.879
> rowVars(tmp5)
[1] 7933.27833 112.28429 89.10593 70.92909 116.36371 78.19666
[7] 59.71561 55.64569 99.50963 44.71906
> rowSd(tmp5)
[1] 89.068953 10.596428 9.439594 8.421941 10.787201 8.842888 7.727587
[8] 7.459604 9.975451 6.687231
> rowMax(tmp5)
[1] 468.96702 92.69237 92.27661 87.92907 99.73967 93.09474 81.52153
[8] 84.03918 89.35775 81.81532
> rowMin(tmp5)
[1] 55.15300 53.93274 58.66946 59.57293 60.13543 53.50292 52.33427 53.08441
[9] 57.32861 53.23691
>
> colMeans(tmp5)
[1] 111.89155 75.12286 73.82615 73.71149 70.39312 69.04094 76.25323
[8] 74.62861 69.75387 71.24529 69.20159 66.50553 67.46361 71.96677
[15] 73.36110 71.16322 71.39313 72.16235 70.94748 73.19673
> colSums(tmp5)
[1] 1118.9155 751.2286 738.2615 737.1149 703.9312 690.4094 762.5323
[8] 746.2861 697.5387 712.4529 692.0159 665.0553 674.6361 719.6677
[15] 733.6110 711.6322 713.9313 721.6235 709.4748 731.9673
> colVars(tmp5)
[1] 15836.44294 66.15992 26.60722 50.75129 56.86522 63.31971
[7] 205.48104 30.92204 53.94305 98.76464 61.80932 71.48340
[13] 32.94604 94.26416 110.20747 136.19430 128.51486 87.26444
[19] 82.13301 103.35156
> colSd(tmp5)
[1] 125.842930 8.133875 5.158219 7.123994 7.540903 7.957369
[7] 14.334610 5.560759 7.344593 9.938040 7.861890 8.454786
[13] 5.739864 9.708973 10.497974 11.670232 11.336439 9.341544
[19] 9.062727 10.166197
> colMax(tmp5)
[1] 468.96702 89.35775 80.72009 85.55435 82.01817 83.36400 99.73967
[8] 83.56849 83.33183 93.58460 81.35329 80.84752 74.58302 85.49631
[15] 86.67525 89.98078 93.09474 85.30054 91.96819 92.69237
> colMin(tmp5)
[1] 52.33427 58.66946 65.31387 63.45242 59.28262 57.78021 53.50292 64.09458
[9] 60.13543 59.69513 58.39924 53.23691 53.93274 53.08441 55.15300 57.07404
[17] 56.76030 56.34518 61.52580 61.97153
>
>
> ### 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] 92.74088 70.88431 70.55779 NA 70.72620 73.08544 67.99556 72.75139
[9] 71.46641 72.04396
> rowSums(tmp5)
[1] 1854.818 1417.686 1411.156 NA 1414.524 1461.709 1359.911 1455.028
[9] 1429.328 1440.879
> rowVars(tmp5)
[1] 7933.27833 112.28429 89.10593 74.85159 116.36371 78.19666
[7] 59.71561 55.64569 99.50963 44.71906
> rowSd(tmp5)
[1] 89.068953 10.596428 9.439594 8.651682 10.787201 8.842888 7.727587
[8] 7.459604 9.975451 6.687231
> rowMax(tmp5)
[1] 468.96702 92.69237 92.27661 NA 99.73967 93.09474 81.52153
[8] 84.03918 89.35775 81.81532
> rowMin(tmp5)
[1] 55.15300 53.93274 58.66946 NA 60.13543 53.50292 52.33427 53.08441
[9] 57.32861 53.23691
>
> colMeans(tmp5)
[1] 111.89155 75.12286 73.82615 73.71149 70.39312 69.04094 76.25323
[8] 74.62861 69.75387 71.24529 69.20159 66.50553 67.46361 71.96677
[15] 73.36110 71.16322 71.39313 72.16235 70.94748 NA
> colSums(tmp5)
[1] 1118.9155 751.2286 738.2615 737.1149 703.9312 690.4094 762.5323
[8] 746.2861 697.5387 712.4529 692.0159 665.0553 674.6361 719.6677
[15] 733.6110 711.6322 713.9313 721.6235 709.4748 NA
> colVars(tmp5)
[1] 15836.44294 66.15992 26.60722 50.75129 56.86522 63.31971
[7] 205.48104 30.92204 53.94305 98.76464 61.80932 71.48340
[13] 32.94604 94.26416 110.20747 136.19430 128.51486 87.26444
[19] 82.13301 NA
> colSd(tmp5)
[1] 125.842930 8.133875 5.158219 7.123994 7.540903 7.957369
[7] 14.334610 5.560759 7.344593 9.938040 7.861890 8.454786
[13] 5.739864 9.708973 10.497974 11.670232 11.336439 9.341544
[19] 9.062727 NA
> colMax(tmp5)
[1] 468.96702 89.35775 80.72009 85.55435 82.01817 83.36400 99.73967
[8] 83.56849 83.33183 93.58460 81.35329 80.84752 74.58302 85.49631
[15] 86.67525 89.98078 93.09474 85.30054 91.96819 NA
> colMin(tmp5)
[1] 52.33427 58.66946 65.31387 63.45242 59.28262 57.78021 53.50292 64.09458
[9] 60.13543 59.69513 58.39924 53.23691 53.93274 53.08441 55.15300 57.07404
[17] 56.76030 56.34518 61.52580 NA
>
> Max(tmp5,na.rm=TRUE)
[1] 468.967
> Min(tmp5,na.rm=TRUE)
[1] 52.33427
> mean(tmp5,na.rm=TRUE)
[1] 73.65512
> Sum(tmp5,na.rm=TRUE)
[1] 14657.37
> Var(tmp5,na.rm=TRUE)
[1] 874.5308
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.74088 70.88431 70.55779 74.33316 70.72620 73.08544 67.99556 72.75139
[9] 71.46641 72.04396
> rowSums(tmp5,na.rm=TRUE)
[1] 1854.818 1417.686 1411.156 1412.330 1414.524 1461.709 1359.911 1455.028
[9] 1429.328 1440.879
> rowVars(tmp5,na.rm=TRUE)
[1] 7933.27833 112.28429 89.10593 74.85159 116.36371 78.19666
[7] 59.71561 55.64569 99.50963 44.71906
> rowSd(tmp5,na.rm=TRUE)
[1] 89.068953 10.596428 9.439594 8.651682 10.787201 8.842888 7.727587
[8] 7.459604 9.975451 6.687231
> rowMax(tmp5,na.rm=TRUE)
[1] 468.96702 92.69237 92.27661 87.92907 99.73967 93.09474 81.52153
[8] 84.03918 89.35775 81.81532
> rowMin(tmp5,na.rm=TRUE)
[1] 55.15300 53.93274 58.66946 59.57293 60.13543 53.50292 52.33427 53.08441
[9] 57.32861 53.23691
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.89155 75.12286 73.82615 73.71149 70.39312 69.04094 76.25323
[8] 74.62861 69.75387 71.24529 69.20159 66.50553 67.46361 71.96677
[15] 73.36110 71.16322 71.39313 72.16235 70.94748 73.00557
> colSums(tmp5,na.rm=TRUE)
[1] 1118.9155 751.2286 738.2615 737.1149 703.9312 690.4094 762.5323
[8] 746.2861 697.5387 712.4529 692.0159 665.0553 674.6361 719.6677
[15] 733.6110 711.6322 713.9313 721.6235 709.4748 657.0501
> colVars(tmp5,na.rm=TRUE)
[1] 15836.44294 66.15992 26.60722 50.75129 56.86522 63.31971
[7] 205.48104 30.92204 53.94305 98.76464 61.80932 71.48340
[13] 32.94604 94.26416 110.20747 136.19430 128.51486 87.26444
[19] 82.13301 115.85942
> colSd(tmp5,na.rm=TRUE)
[1] 125.842930 8.133875 5.158219 7.123994 7.540903 7.957369
[7] 14.334610 5.560759 7.344593 9.938040 7.861890 8.454786
[13] 5.739864 9.708973 10.497974 11.670232 11.336439 9.341544
[19] 9.062727 10.763801
> colMax(tmp5,na.rm=TRUE)
[1] 468.96702 89.35775 80.72009 85.55435 82.01817 83.36400 99.73967
[8] 83.56849 83.33183 93.58460 81.35329 80.84752 74.58302 85.49631
[15] 86.67525 89.98078 93.09474 85.30054 91.96819 92.69237
> colMin(tmp5,na.rm=TRUE)
[1] 52.33427 58.66946 65.31387 63.45242 59.28262 57.78021 53.50292 64.09458
[9] 60.13543 59.69513 58.39924 53.23691 53.93274 53.08441 55.15300 57.07404
[17] 56.76030 56.34518 61.52580 61.97153
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.74088 70.88431 70.55779 NaN 70.72620 73.08544 67.99556 72.75139
[9] 71.46641 72.04396
> rowSums(tmp5,na.rm=TRUE)
[1] 1854.818 1417.686 1411.156 0.000 1414.524 1461.709 1359.911 1455.028
[9] 1429.328 1440.879
> rowVars(tmp5,na.rm=TRUE)
[1] 7933.27833 112.28429 89.10593 NA 116.36371 78.19666
[7] 59.71561 55.64569 99.50963 44.71906
> rowSd(tmp5,na.rm=TRUE)
[1] 89.068953 10.596428 9.439594 NA 10.787201 8.842888 7.727587
[8] 7.459604 9.975451 6.687231
> rowMax(tmp5,na.rm=TRUE)
[1] 468.96702 92.69237 92.27661 NA 99.73967 93.09474 81.52153
[8] 84.03918 89.35775 81.81532
> rowMin(tmp5,na.rm=TRUE)
[1] 55.15300 53.93274 58.66946 NA 60.13543 53.50292 52.33427 53.08441
[9] 57.32861 53.23691
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.87352 75.65269 74.65954 73.01690 71.15227 68.13902 76.08494
[8] 74.66243 70.79604 70.73657 67.85140 67.27582 67.39026 71.49676
[15] 72.18908 69.30035 71.10969 70.70255 71.57560 NaN
> colSums(tmp5,na.rm=TRUE)
[1] 1033.8616 680.8743 671.9359 657.1521 640.3704 613.2512 684.7644
[8] 671.9619 637.1643 636.6291 610.6626 605.4823 606.5123 643.4708
[15] 649.7017 623.7031 639.9872 636.3230 644.1804 0.0000
> colVars(tmp5,na.rm=TRUE)
[1] 17715.96186 71.27180 22.11956 51.66767 57.48987 62.08324
[7] 230.84754 34.77442 48.46731 108.19874 49.02663 73.74370
[13] 37.00376 103.56191 108.53009 114.17780 143.67542 74.19860
[19] 87.96112 NA
> colSd(tmp5,na.rm=TRUE)
[1] 133.101322 8.442263 4.703144 7.188022 7.582207 7.879292
[7] 15.193668 5.896984 6.961847 10.401862 7.001902 8.587415
[13] 6.083072 10.176537 10.417777 10.685401 11.986468 8.613861
[19] 9.378759 NA
> colMax(tmp5,na.rm=TRUE)
[1] 468.96702 89.35775 80.72009 85.55435 82.01817 83.36400 99.73967
[8] 83.56849 83.33183 93.58460 76.29660 80.84752 74.58302 85.49631
[15] 86.67525 89.98078 93.09474 81.81532 91.96819 -Inf
> colMin(tmp5,na.rm=TRUE)
[1] 52.33427 58.66946 65.31387 63.45242 59.28262 57.78021 53.50292 64.09458
[9] 60.13543 59.69513 58.39924 53.23691 53.93274 53.08441 55.15300 57.07404
[17] 56.76030 56.34518 61.52580 Inf
>
>
>
>
> 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] 245.3948 313.9799 282.9187 222.1367 164.8468 148.2679 233.4572 250.6056
[9] 221.5752 255.5513
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 245.3948 313.9799 282.9187 222.1367 164.8468 148.2679 233.4572 250.6056
[9] 221.5752 255.5513
>
>
>
> 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 2.842171e-14 0.000000e+00 5.684342e-14 1.136868e-13
[6] 1.705303e-13 -5.684342e-14 5.684342e-14 5.684342e-14 1.705303e-13
[11] 1.136868e-13 -5.684342e-14 -2.842171e-14 0.000000e+00 1.421085e-14
[16] -8.526513e-14 -5.684342e-14 1.421085e-14 -5.684342e-14 2.842171e-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)
+ }
2 17
10 15
6 5
2 5
10 13
3 18
2 9
5 6
8 3
1 7
7 19
4 14
4 20
10 17
8 17
10 20
3 2
10 4
7 15
7 16
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] 2.160665
> Min(tmp)
[1] -2.214159
> mean(tmp)
[1] 0.04834552
> Sum(tmp)
[1] 4.834552
> Var(tmp)
[1] 0.803858
>
> rowMeans(tmp)
[1] 0.04834552
> rowSums(tmp)
[1] 4.834552
> rowVars(tmp)
[1] 0.803858
> rowSd(tmp)
[1] 0.8965813
> rowMax(tmp)
[1] 2.160665
> rowMin(tmp)
[1] -2.214159
>
> colMeans(tmp)
[1] 0.69456007 0.53211127 -0.42958460 1.18646670 0.16556833 1.77440345
[7] 0.61735559 0.51943326 0.47984414 0.97564374 -0.38960207 -1.70278760
[13] -0.35505819 -1.03996029 -0.05510415 -0.34250110 0.46000383 -0.88579586
[19] -0.18573937 -0.16066316 0.11400674 1.30419002 0.30576892 0.46018270
[25] 0.69521716 -0.23630315 0.37387995 -0.98030871 -0.73595978 1.22882632
[31] 0.89916544 0.68478368 1.09342235 1.27787675 -1.32224214 2.16066473
[37] 0.80203972 0.42678062 -1.08706894 -0.07257875 1.06558660 0.25859956
[43] -1.16120770 -0.40641955 0.57425092 1.73936734 -1.40294522 1.12716926
[49] 0.75601985 -0.49135371 -0.23521368 -1.71515186 0.14490996 -2.21415915
[55] -0.79877567 0.90702271 -0.75380555 1.22075437 -0.67547669 -0.20286697
[61] -2.20487117 -0.11726474 0.69350677 0.64452608 -0.33161067 1.22377436
[67] -0.02834487 -0.18671104 -0.43211753 0.58166931 -0.35826418 -1.63804429
[73] 0.06508196 -0.77140876 0.55057651 0.45481694 -0.06537184 0.03199642
[79] 0.28394746 -0.37679511 -0.92011058 0.48689550 0.12663508 -0.17796814
[85] 0.08411981 -0.01566197 0.99305867 0.81334229 -0.72455846 0.67912082
[91] -1.17306111 -0.65159164 -0.53891533 -1.51130090 1.98829831 0.20606249
[97] -1.00181649 0.14358337 -0.17029614 1.19238289
> colSums(tmp)
[1] 0.69456007 0.53211127 -0.42958460 1.18646670 0.16556833 1.77440345
[7] 0.61735559 0.51943326 0.47984414 0.97564374 -0.38960207 -1.70278760
[13] -0.35505819 -1.03996029 -0.05510415 -0.34250110 0.46000383 -0.88579586
[19] -0.18573937 -0.16066316 0.11400674 1.30419002 0.30576892 0.46018270
[25] 0.69521716 -0.23630315 0.37387995 -0.98030871 -0.73595978 1.22882632
[31] 0.89916544 0.68478368 1.09342235 1.27787675 -1.32224214 2.16066473
[37] 0.80203972 0.42678062 -1.08706894 -0.07257875 1.06558660 0.25859956
[43] -1.16120770 -0.40641955 0.57425092 1.73936734 -1.40294522 1.12716926
[49] 0.75601985 -0.49135371 -0.23521368 -1.71515186 0.14490996 -2.21415915
[55] -0.79877567 0.90702271 -0.75380555 1.22075437 -0.67547669 -0.20286697
[61] -2.20487117 -0.11726474 0.69350677 0.64452608 -0.33161067 1.22377436
[67] -0.02834487 -0.18671104 -0.43211753 0.58166931 -0.35826418 -1.63804429
[73] 0.06508196 -0.77140876 0.55057651 0.45481694 -0.06537184 0.03199642
[79] 0.28394746 -0.37679511 -0.92011058 0.48689550 0.12663508 -0.17796814
[85] 0.08411981 -0.01566197 0.99305867 0.81334229 -0.72455846 0.67912082
[91] -1.17306111 -0.65159164 -0.53891533 -1.51130090 1.98829831 0.20606249
[97] -1.00181649 0.14358337 -0.17029614 1.19238289
> 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] 0.69456007 0.53211127 -0.42958460 1.18646670 0.16556833 1.77440345
[7] 0.61735559 0.51943326 0.47984414 0.97564374 -0.38960207 -1.70278760
[13] -0.35505819 -1.03996029 -0.05510415 -0.34250110 0.46000383 -0.88579586
[19] -0.18573937 -0.16066316 0.11400674 1.30419002 0.30576892 0.46018270
[25] 0.69521716 -0.23630315 0.37387995 -0.98030871 -0.73595978 1.22882632
[31] 0.89916544 0.68478368 1.09342235 1.27787675 -1.32224214 2.16066473
[37] 0.80203972 0.42678062 -1.08706894 -0.07257875 1.06558660 0.25859956
[43] -1.16120770 -0.40641955 0.57425092 1.73936734 -1.40294522 1.12716926
[49] 0.75601985 -0.49135371 -0.23521368 -1.71515186 0.14490996 -2.21415915
[55] -0.79877567 0.90702271 -0.75380555 1.22075437 -0.67547669 -0.20286697
[61] -2.20487117 -0.11726474 0.69350677 0.64452608 -0.33161067 1.22377436
[67] -0.02834487 -0.18671104 -0.43211753 0.58166931 -0.35826418 -1.63804429
[73] 0.06508196 -0.77140876 0.55057651 0.45481694 -0.06537184 0.03199642
[79] 0.28394746 -0.37679511 -0.92011058 0.48689550 0.12663508 -0.17796814
[85] 0.08411981 -0.01566197 0.99305867 0.81334229 -0.72455846 0.67912082
[91] -1.17306111 -0.65159164 -0.53891533 -1.51130090 1.98829831 0.20606249
[97] -1.00181649 0.14358337 -0.17029614 1.19238289
> colMin(tmp)
[1] 0.69456007 0.53211127 -0.42958460 1.18646670 0.16556833 1.77440345
[7] 0.61735559 0.51943326 0.47984414 0.97564374 -0.38960207 -1.70278760
[13] -0.35505819 -1.03996029 -0.05510415 -0.34250110 0.46000383 -0.88579586
[19] -0.18573937 -0.16066316 0.11400674 1.30419002 0.30576892 0.46018270
[25] 0.69521716 -0.23630315 0.37387995 -0.98030871 -0.73595978 1.22882632
[31] 0.89916544 0.68478368 1.09342235 1.27787675 -1.32224214 2.16066473
[37] 0.80203972 0.42678062 -1.08706894 -0.07257875 1.06558660 0.25859956
[43] -1.16120770 -0.40641955 0.57425092 1.73936734 -1.40294522 1.12716926
[49] 0.75601985 -0.49135371 -0.23521368 -1.71515186 0.14490996 -2.21415915
[55] -0.79877567 0.90702271 -0.75380555 1.22075437 -0.67547669 -0.20286697
[61] -2.20487117 -0.11726474 0.69350677 0.64452608 -0.33161067 1.22377436
[67] -0.02834487 -0.18671104 -0.43211753 0.58166931 -0.35826418 -1.63804429
[73] 0.06508196 -0.77140876 0.55057651 0.45481694 -0.06537184 0.03199642
[79] 0.28394746 -0.37679511 -0.92011058 0.48689550 0.12663508 -0.17796814
[85] 0.08411981 -0.01566197 0.99305867 0.81334229 -0.72455846 0.67912082
[91] -1.17306111 -0.65159164 -0.53891533 -1.51130090 1.98829831 0.20606249
[97] -1.00181649 0.14358337 -0.17029614 1.19238289
> colMedians(tmp)
[1] 0.69456007 0.53211127 -0.42958460 1.18646670 0.16556833 1.77440345
[7] 0.61735559 0.51943326 0.47984414 0.97564374 -0.38960207 -1.70278760
[13] -0.35505819 -1.03996029 -0.05510415 -0.34250110 0.46000383 -0.88579586
[19] -0.18573937 -0.16066316 0.11400674 1.30419002 0.30576892 0.46018270
[25] 0.69521716 -0.23630315 0.37387995 -0.98030871 -0.73595978 1.22882632
[31] 0.89916544 0.68478368 1.09342235 1.27787675 -1.32224214 2.16066473
[37] 0.80203972 0.42678062 -1.08706894 -0.07257875 1.06558660 0.25859956
[43] -1.16120770 -0.40641955 0.57425092 1.73936734 -1.40294522 1.12716926
[49] 0.75601985 -0.49135371 -0.23521368 -1.71515186 0.14490996 -2.21415915
[55] -0.79877567 0.90702271 -0.75380555 1.22075437 -0.67547669 -0.20286697
[61] -2.20487117 -0.11726474 0.69350677 0.64452608 -0.33161067 1.22377436
[67] -0.02834487 -0.18671104 -0.43211753 0.58166931 -0.35826418 -1.63804429
[73] 0.06508196 -0.77140876 0.55057651 0.45481694 -0.06537184 0.03199642
[79] 0.28394746 -0.37679511 -0.92011058 0.48689550 0.12663508 -0.17796814
[85] 0.08411981 -0.01566197 0.99305867 0.81334229 -0.72455846 0.67912082
[91] -1.17306111 -0.65159164 -0.53891533 -1.51130090 1.98829831 0.20606249
[97] -1.00181649 0.14358337 -0.17029614 1.19238289
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.6945601 0.5321113 -0.4295846 1.186467 0.1655683 1.774403 0.6173556
[2,] 0.6945601 0.5321113 -0.4295846 1.186467 0.1655683 1.774403 0.6173556
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.5194333 0.4798441 0.9756437 -0.3896021 -1.702788 -0.3550582 -1.03996
[2,] 0.5194333 0.4798441 0.9756437 -0.3896021 -1.702788 -0.3550582 -1.03996
[,15] [,16] [,17] [,18] [,19] [,20]
[1,] -0.05510415 -0.3425011 0.4600038 -0.8857959 -0.1857394 -0.1606632
[2,] -0.05510415 -0.3425011 0.4600038 -0.8857959 -0.1857394 -0.1606632
[,21] [,22] [,23] [,24] [,25] [,26] [,27]
[1,] 0.1140067 1.30419 0.3057689 0.4601827 0.6952172 -0.2363031 0.37388
[2,] 0.1140067 1.30419 0.3057689 0.4601827 0.6952172 -0.2363031 0.37388
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] -0.9803087 -0.7359598 1.228826 0.8991654 0.6847837 1.093422 1.277877
[2,] -0.9803087 -0.7359598 1.228826 0.8991654 0.6847837 1.093422 1.277877
[,35] [,36] [,37] [,38] [,39] [,40] [,41]
[1,] -1.322242 2.160665 0.8020397 0.4267806 -1.087069 -0.07257875 1.065587
[2,] -1.322242 2.160665 0.8020397 0.4267806 -1.087069 -0.07257875 1.065587
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 0.2585996 -1.161208 -0.4064196 0.5742509 1.739367 -1.402945 1.127169
[2,] 0.2585996 -1.161208 -0.4064196 0.5742509 1.739367 -1.402945 1.127169
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] 0.7560198 -0.4913537 -0.2352137 -1.715152 0.14491 -2.214159 -0.7987757
[2,] 0.7560198 -0.4913537 -0.2352137 -1.715152 0.14491 -2.214159 -0.7987757
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] 0.9070227 -0.7538055 1.220754 -0.6754767 -0.202867 -2.204871 -0.1172647
[2,] 0.9070227 -0.7538055 1.220754 -0.6754767 -0.202867 -2.204871 -0.1172647
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] 0.6935068 0.6445261 -0.3316107 1.223774 -0.02834487 -0.186711 -0.4321175
[2,] 0.6935068 0.6445261 -0.3316107 1.223774 -0.02834487 -0.186711 -0.4321175
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] 0.5816693 -0.3582642 -1.638044 0.06508196 -0.7714088 0.5505765 0.4548169
[2,] 0.5816693 -0.3582642 -1.638044 0.06508196 -0.7714088 0.5505765 0.4548169
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -0.06537184 0.03199642 0.2839475 -0.3767951 -0.9201106 0.4868955 0.1266351
[2,] -0.06537184 0.03199642 0.2839475 -0.3767951 -0.9201106 0.4868955 0.1266351
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.1779681 0.08411981 -0.01566197 0.9930587 0.8133423 -0.7245585 0.6791208
[2,] -0.1779681 0.08411981 -0.01566197 0.9930587 0.8133423 -0.7245585 0.6791208
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] -1.173061 -0.6515916 -0.5389153 -1.511301 1.988298 0.2060625 -1.001816
[2,] -1.173061 -0.6515916 -0.5389153 -1.511301 1.988298 0.2060625 -1.001816
[,98] [,99] [,100]
[1,] 0.1435834 -0.1702961 1.192383
[2,] 0.1435834 -0.1702961 1.192383
>
>
> Max(tmp2)
[1] 2.205815
> Min(tmp2)
[1] -2.746182
> mean(tmp2)
[1] -0.01918121
> Sum(tmp2)
[1] -1.918121
> Var(tmp2)
[1] 0.98126
>
> rowMeans(tmp2)
[1] -0.22717240 -0.01377005 0.84752733 0.13907351 1.42134476 0.48553081
[7] 1.02900325 0.36306409 0.01106533 -0.32933456 0.20100200 0.85162201
[13] -0.89022780 -1.36845269 -0.37913553 2.20581519 -0.31544784 -0.72143683
[19] -0.40793358 0.12777586 1.34389559 1.49054071 1.02217165 -1.57086928
[25] 0.66712582 -0.32359163 -1.05057811 1.11986719 0.79254640 -0.66382106
[31] -0.55842814 0.44686764 1.01897458 -0.49501449 0.70359981 -0.34593519
[37] 1.25522059 0.66439529 -2.50963209 -0.09458713 -0.64050818 -0.88453531
[43] 1.02711737 -2.74618187 0.93357203 -1.03997538 -0.51749846 -1.59897798
[49] -0.84123897 0.18139688 -2.20415990 0.29986662 1.14100036 0.98888359
[55] 0.92948089 -0.97272276 0.68313891 0.49426992 0.60801696 0.18022782
[61] -0.27189965 -1.63988328 0.59093400 0.31325555 -0.25005814 -0.19722436
[67] -0.34546331 0.98752471 0.91065131 0.84897904 -1.03249944 0.28141117
[73] -0.03282338 -0.60355620 -1.79615677 0.45438249 -0.97248935 -0.94292631
[79] 0.02558423 1.27985704 -0.45429229 0.18430850 -0.31346300 -0.96672017
[85] 0.85918229 -0.43072523 -2.16715741 0.19677396 0.82703783 0.35711552
[91] 1.18439536 1.13839304 0.64220023 -1.67174978 -0.05365167 0.03601319
[97] 1.05120729 0.52093453 -2.54331622 0.11396002
> rowSums(tmp2)
[1] -0.22717240 -0.01377005 0.84752733 0.13907351 1.42134476 0.48553081
[7] 1.02900325 0.36306409 0.01106533 -0.32933456 0.20100200 0.85162201
[13] -0.89022780 -1.36845269 -0.37913553 2.20581519 -0.31544784 -0.72143683
[19] -0.40793358 0.12777586 1.34389559 1.49054071 1.02217165 -1.57086928
[25] 0.66712582 -0.32359163 -1.05057811 1.11986719 0.79254640 -0.66382106
[31] -0.55842814 0.44686764 1.01897458 -0.49501449 0.70359981 -0.34593519
[37] 1.25522059 0.66439529 -2.50963209 -0.09458713 -0.64050818 -0.88453531
[43] 1.02711737 -2.74618187 0.93357203 -1.03997538 -0.51749846 -1.59897798
[49] -0.84123897 0.18139688 -2.20415990 0.29986662 1.14100036 0.98888359
[55] 0.92948089 -0.97272276 0.68313891 0.49426992 0.60801696 0.18022782
[61] -0.27189965 -1.63988328 0.59093400 0.31325555 -0.25005814 -0.19722436
[67] -0.34546331 0.98752471 0.91065131 0.84897904 -1.03249944 0.28141117
[73] -0.03282338 -0.60355620 -1.79615677 0.45438249 -0.97248935 -0.94292631
[79] 0.02558423 1.27985704 -0.45429229 0.18430850 -0.31346300 -0.96672017
[85] 0.85918229 -0.43072523 -2.16715741 0.19677396 0.82703783 0.35711552
[91] 1.18439536 1.13839304 0.64220023 -1.67174978 -0.05365167 0.03601319
[97] 1.05120729 0.52093453 -2.54331622 0.11396002
> 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] -0.22717240 -0.01377005 0.84752733 0.13907351 1.42134476 0.48553081
[7] 1.02900325 0.36306409 0.01106533 -0.32933456 0.20100200 0.85162201
[13] -0.89022780 -1.36845269 -0.37913553 2.20581519 -0.31544784 -0.72143683
[19] -0.40793358 0.12777586 1.34389559 1.49054071 1.02217165 -1.57086928
[25] 0.66712582 -0.32359163 -1.05057811 1.11986719 0.79254640 -0.66382106
[31] -0.55842814 0.44686764 1.01897458 -0.49501449 0.70359981 -0.34593519
[37] 1.25522059 0.66439529 -2.50963209 -0.09458713 -0.64050818 -0.88453531
[43] 1.02711737 -2.74618187 0.93357203 -1.03997538 -0.51749846 -1.59897798
[49] -0.84123897 0.18139688 -2.20415990 0.29986662 1.14100036 0.98888359
[55] 0.92948089 -0.97272276 0.68313891 0.49426992 0.60801696 0.18022782
[61] -0.27189965 -1.63988328 0.59093400 0.31325555 -0.25005814 -0.19722436
[67] -0.34546331 0.98752471 0.91065131 0.84897904 -1.03249944 0.28141117
[73] -0.03282338 -0.60355620 -1.79615677 0.45438249 -0.97248935 -0.94292631
[79] 0.02558423 1.27985704 -0.45429229 0.18430850 -0.31346300 -0.96672017
[85] 0.85918229 -0.43072523 -2.16715741 0.19677396 0.82703783 0.35711552
[91] 1.18439536 1.13839304 0.64220023 -1.67174978 -0.05365167 0.03601319
[97] 1.05120729 0.52093453 -2.54331622 0.11396002
> rowMin(tmp2)
[1] -0.22717240 -0.01377005 0.84752733 0.13907351 1.42134476 0.48553081
[7] 1.02900325 0.36306409 0.01106533 -0.32933456 0.20100200 0.85162201
[13] -0.89022780 -1.36845269 -0.37913553 2.20581519 -0.31544784 -0.72143683
[19] -0.40793358 0.12777586 1.34389559 1.49054071 1.02217165 -1.57086928
[25] 0.66712582 -0.32359163 -1.05057811 1.11986719 0.79254640 -0.66382106
[31] -0.55842814 0.44686764 1.01897458 -0.49501449 0.70359981 -0.34593519
[37] 1.25522059 0.66439529 -2.50963209 -0.09458713 -0.64050818 -0.88453531
[43] 1.02711737 -2.74618187 0.93357203 -1.03997538 -0.51749846 -1.59897798
[49] -0.84123897 0.18139688 -2.20415990 0.29986662 1.14100036 0.98888359
[55] 0.92948089 -0.97272276 0.68313891 0.49426992 0.60801696 0.18022782
[61] -0.27189965 -1.63988328 0.59093400 0.31325555 -0.25005814 -0.19722436
[67] -0.34546331 0.98752471 0.91065131 0.84897904 -1.03249944 0.28141117
[73] -0.03282338 -0.60355620 -1.79615677 0.45438249 -0.97248935 -0.94292631
[79] 0.02558423 1.27985704 -0.45429229 0.18430850 -0.31346300 -0.96672017
[85] 0.85918229 -0.43072523 -2.16715741 0.19677396 0.82703783 0.35711552
[91] 1.18439536 1.13839304 0.64220023 -1.67174978 -0.05365167 0.03601319
[97] 1.05120729 0.52093453 -2.54331622 0.11396002
>
> colMeans(tmp2)
[1] -0.01918121
> colSums(tmp2)
[1] -1.918121
> colVars(tmp2)
[1] 0.98126
> colSd(tmp2)
[1] 0.9905857
> colMax(tmp2)
[1] 2.205815
> colMin(tmp2)
[1] -2.746182
> colMedians(tmp2)
[1] 0.1208679
> colRanges(tmp2)
[,1]
[1,] -2.746182
[2,] 2.205815
>
> 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] 3.3426932 -0.5418762 0.4782996 -2.6684068 -1.3885786 1.1284381
[7] 1.8986589 -3.5208368 -1.0323505 4.9116501
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.3711708
[2,] -0.1918287
[3,] 0.6141501
[4,] 0.9261905
[5,] 1.2286044
>
> rowApply(tmp,sum)
[1] 1.6200912 -2.9004246 -2.2401757 -0.5927155 5.7619135 -1.8591160
[7] -2.1875889 3.7204562 2.4382114 -1.1529605
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 5 9 8 8 9 5 7 7 10
[2,] 1 2 8 3 3 8 7 10 10 4
[3,] 9 8 6 4 4 10 6 2 6 3
[4,] 5 6 7 5 7 7 1 5 4 1
[5,] 7 3 4 2 5 2 10 6 3 7
[6,] 3 4 1 10 9 3 8 9 2 2
[7,] 8 10 3 7 2 5 4 8 1 8
[8,] 6 7 5 9 1 1 2 1 5 5
[9,] 4 1 2 1 10 6 3 3 9 9
[10,] 10 9 10 6 6 4 9 4 8 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -4.3847246 0.6275880 3.3282230 -1.5055523 2.2739646 -2.6810145
[7] 0.5314789 0.1828965 1.1484144 0.9488509 -5.1329065 2.4482208
[13] 1.8559030 1.7497783 -2.1126610 -0.6304907 -0.8962723 -2.4585903
[19] 2.2412982 -2.1940126
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5555590
[2,] -1.0492570
[3,] -0.8690680
[4,] -0.7063813
[5,] -0.2044594
>
> rowApply(tmp,sum)
[1] 2.5205262 -0.7899921 -4.9184712 1.3667629 -2.8384339
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 2 7 13 6 3
[2,] 16 10 17 14 4
[3,] 13 16 9 16 19
[4,] 14 13 4 7 1
[5,] 7 15 10 15 20
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.5555590 0.6686532 0.5285698 0.5708047 -0.2113187 -1.23212238
[2,] -0.7063813 -0.3477692 1.3407450 0.2231069 0.6905868 0.08241919
[3,] -0.2044594 0.7748462 -0.4778919 -0.7990317 -0.4464202 -1.58367768
[4,] -0.8690680 0.4963162 0.7980978 -0.1957030 0.6408276 0.20127744
[5,] -1.0492570 -0.9644583 1.1387023 -1.3047292 1.6002892 -0.14891108
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.9198580 0.84373899 -0.3304535 0.4608019 -1.69045810 0.4233347
[2,] -0.4985216 1.43193503 -1.2269753 0.5712449 -1.51098196 2.2368988
[3,] 0.1626579 0.07004347 1.2366871 0.2928997 -0.37598917 -0.6371940
[4,] 0.4601893 -1.51926048 2.0935532 -1.0535337 -1.52671882 0.8377790
[5,] -0.5127046 -0.64356054 -0.6243971 0.6774380 -0.02875844 -0.4125977
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.1727378 1.2834392 0.1795865 -0.4273339 0.4585302 -0.396137150
[2,] 1.6910203 -1.7586987 -0.8980531 1.3785033 -1.1970256 -0.004819184
[3,] -0.3754719 1.3693717 -0.4967927 -0.8175275 -0.4842432 -2.342666706
[4,] -0.1636702 1.5458168 -1.1731232 -1.5633208 1.4155790 0.178893841
[5,] 0.8767626 -0.6901508 0.2757215 0.7991882 -1.0891127 0.106138936
[,19] [,20]
[1,] 1.6021599 0.5971697
[2,] -0.4426998 -1.8445266
[3,] 0.8208388 -0.6044501
[4,] 0.4331700 0.3296608
[5,] -0.1721707 -0.6718664
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/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: /home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/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 -0.06690736 0.987725 -1.630803 0.2345701 1.642688 0.5957768 -0.4321383
col8 col9 col10 col11 col12 col13 col14
row1 -0.7923598 -1.475619 0.6821998 0.02011811 0.07664734 0.8272125 0.2744857
col15 col16 col17 col18 col19 col20
row1 0.2482057 -2.379183 2.219012 -1.17332 0.5999736 -0.7996391
> tmp[,"col10"]
col10
row1 0.68219985
row2 0.93443942
row3 -2.16453300
row4 -0.07020763
row5 0.63556286
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.06690736 0.9877250 -1.6308029 0.2345701 1.6426881 0.5957768
row5 0.37828897 0.7303399 0.2397252 -0.9296621 -0.1622884 0.8169423
col7 col8 col9 col10 col11 col12 col13
row1 -0.4321383 -0.7923598 -1.4756186 0.6821998 0.02011811 0.07664734 0.8272125
row5 -0.4411589 1.5317973 0.9467835 0.6355629 0.19525223 0.96491909 1.1559894
col14 col15 col16 col17 col18 col19
row1 0.2744857 0.2482057 -2.3791834 2.2190124 -1.1733200 0.5999736
row5 -1.1877277 0.1921126 0.0566949 -0.3607825 0.1408807 -0.3329267
col20
row1 -0.7996391
row5 -0.7328395
> tmp[,c("col6","col20")]
col6 col20
row1 0.5957768 -0.79963907
row2 -0.6909428 0.18205166
row3 0.3046088 0.83499215
row4 -1.1971656 -0.05900803
row5 0.8169423 -0.73283945
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.5957768 -0.7996391
row5 0.8169423 -0.7328395
>
>
>
>
> 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 50.07645 49.76688 49.27152 49.6248 48.1354 106.1169 50.25932 51.9926
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.88789 47.51894 49.61525 51.72131 49.3988 49.1669 49.32533 50.09426
col17 col18 col19 col20
row1 49.27721 48.6638 51.84246 103.8783
> tmp[,"col10"]
col10
row1 47.51894
row2 31.62015
row3 31.26005
row4 29.71460
row5 49.74034
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.07645 49.76688 49.27152 49.62480 48.13540 106.1169 50.25932 51.99260
row5 49.44492 48.62197 48.90192 50.36913 47.60354 104.5907 49.62253 50.94293
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.88789 47.51894 49.61525 51.72131 49.39880 49.16690 49.32533 50.09426
row5 50.15923 49.74034 50.04188 51.86688 47.89607 49.17934 50.71753 50.18320
col17 col18 col19 col20
row1 49.27721 48.66380 51.84246 103.8783
row5 49.20951 50.61442 49.06218 106.8586
> tmp[,c("col6","col20")]
col6 col20
row1 106.11688 103.87831
row2 77.01662 75.42522
row3 74.93772 77.34694
row4 74.77878 73.14213
row5 104.59065 106.85856
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 106.1169 103.8783
row5 104.5907 106.8586
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 106.1169 103.8783
row5 104.5907 106.8586
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.766455994
[2,] -2.282834421
[3,] 0.006193766
[4,] -0.547688752
[5,] 0.366368301
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.33316939 1.8209558
[2,] -0.69625029 0.4114156
[3,] -1.42431663 0.3895957
[4,] -0.05341274 0.2097664
[5,] -0.81886693 -0.4946588
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.5022038 -2.1532237
[2,] 0.7880199 -1.3152374
[3,] -1.3093022 -0.9792540
[4,] 0.2173304 0.4532827
[5,] 1.3803373 0.4562683
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.5022038
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.5022038
[2,] 0.7880199
>
>
>
> 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] [,7]
row3 -3.1954276 0.7641197 0.7997502 -1.1256970 -0.1989044 -0.9830407 -1.623295
row1 0.7367581 0.4271844 -0.6263938 0.5393967 -0.4867754 -0.2837183 1.486447
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.765207 0.7275225 -1.7643786 0.2523786 -0.5471174 -0.7351623 0.06845916
row1 2.766970 -0.2686857 -0.1794388 0.5398627 0.3409899 -1.2236532 0.40270873
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.9049061 1.328876 -0.9874476 -1.7192011 0.2117793 -0.2603964
row1 1.3240526 -1.222290 -0.4351368 0.3490706 -1.5237395 0.4024818
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.3617999 0.6380901 0.5752787 1.541285 1.761808 1.216951 -1.357863
[,8] [,9] [,10]
row2 0.702911 0.4520654 -0.3681474
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.9119948 0.7363349 -0.1598844 -1.375255 1.783384 0.696316 0.5377753
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.6286905 -0.3066748 -0.2171766 1.239187 -1.014204 -0.4892248 -1.977608
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.498832 0.8749337 0.2766525 0.06378598 -0.2636055 2.126493
>
>
> 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: 0x56264bee3be0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3136b9f1"
[2] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c37d855c04"
[3] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c35a7add4d"
[4] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c31ee1b47"
[5] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c31e20091b"
[6] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c34d80a2a2"
[7] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c34816c7c6"
[8] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3369fa34"
[9] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3103d830f"
[10] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3e723ee0"
[11] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3282e0cad"
[12] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c34e855fff"
[13] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c35c28ca12"
[14] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c357ee8336"
[15] "/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests/BM2193c3141c74b1"
>
>
> ### 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: 0x56264d23ea90>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x56264d23ea90>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x56264d23ea90>
> rowMedians(tmp)
[1] 0.119331042 -0.239380233 0.095319509 -0.060741046 0.072300912
[6] -0.081858986 0.547287205 -0.076580186 -0.373731235 -0.129074632
[11] 0.248541370 -0.095712475 -0.029092617 0.184962242 -0.047342481
[16] -0.086073770 0.319663481 -0.016190919 0.277456920 0.114227921
[21] -0.342770113 1.259857303 0.313135764 0.581030843 -0.144806336
[26] 0.545035887 -0.460403465 -0.021964018 -0.257637016 0.204011446
[31] 0.109967447 0.122911810 -0.126502331 -0.415172009 -0.311413642
[36] -0.002460268 -0.019661868 0.651482441 0.141197279 -0.295443381
[41] 0.485049447 0.333513878 0.152963942 -0.143643602 -0.206120095
[46] 0.250007175 0.152312470 -0.002712064 -0.018875932 -0.150492191
[51] 0.100973487 -0.566551672 0.701259155 0.443727976 -0.061648973
[56] -0.281818067 -0.274832083 0.411541301 0.082844273 0.078914775
[61] 0.008221574 -0.038901892 0.135462102 -0.174628323 0.069161512
[66] 0.642094698 -0.203468227 -0.230657535 0.692712415 0.052103349
[71] 0.287119976 -0.210973510 0.189187523 0.072199028 -0.339356451
[76] -0.147500777 0.526825334 0.110061230 -0.149514706 0.059944230
[81] 0.635946355 -0.112312537 0.436061770 -0.436860227 -0.245201009
[86] 0.445181685 0.038427139 -0.148144848 -0.022531593 0.010614616
[91] 0.214565255 -0.490144103 -0.102147017 0.399778771 0.123687229
[96] -0.111209548 0.330970274 -0.089378271 -0.131333970 0.002252879
[101] -0.039082932 -0.135211635 -0.679144765 0.486344278 0.287623264
[106] -0.121985273 0.239459459 0.213437728 0.179944108 0.027031238
[111] 0.188487250 -0.048181493 0.055037779 0.267827637 0.403075441
[116] 0.252899252 -0.223919125 0.185174721 0.289561707 -0.281366715
[121] -0.343579942 -0.166937505 -0.636140257 -0.030839863 -0.266519702
[126] -0.041558146 -0.036166662 0.093560094 0.214385588 0.426390141
[131] -0.458508745 -0.359369421 0.305261660 -0.378313263 0.046961182
[136] -0.052847480 -0.234502463 -0.416299896 0.311412639 0.611459560
[141] 0.502523273 0.057305275 -0.571688720 -0.016480208 -0.232063628
[146] 0.294418054 -0.060588246 0.325292763 -0.215306481 -0.346119716
[151] -0.151387599 0.071071854 -0.606436707 -0.436294128 -0.244752960
[156] -0.167350909 0.075881376 0.451851444 -0.471039563 -0.847108672
[161] 0.547208383 0.056907368 0.487641043 -0.425080697 -0.130023236
[166] -0.355600939 0.120347071 -0.228610680 0.502019461 0.352282121
[171] -0.300071359 0.100319854 -0.836419973 0.357767763 0.314832277
[176] 0.218753736 -0.128335325 0.266129274 -0.113976791 -0.030422178
[181] 0.322669149 -0.108480626 -0.047012007 -0.088076368 0.256478006
[186] 0.426376094 0.190392343 -0.128038075 0.453170454 0.448834215
[191] -0.270637153 -0.459364029 -0.202072113 -0.462068198 -0.045091933
[196] 0.177375009 0.052959295 0.430404003 -0.512129242 0.238348145
[201] 0.109915956 0.051317084 0.005084460 0.235220008 0.376881954
[206] -0.017617164 0.107281745 0.332358404 -0.186257794 -0.103553528
[211] -0.025156240 0.385424036 -0.525016125 -0.011184453 0.123079829
[216] 0.409436600 -0.229160935 0.443743455 0.267193853 -0.447611789
[221] -0.150198758 0.024235976 0.307346775 -0.460373386 0.105818162
[226] 0.164073081 0.359073338 -0.280474710 -0.467809249 0.239087641
>
> proc.time()
user system elapsed
1.376 1.513 2.903
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 0x558f625791a0>
> .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: 0x558f625791a0>
> .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: 0x558f625791a0>
> .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: 0x558f625791a0>
> 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: 0x558f61f4f440>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f61f4f440>
> .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: 0x558f61f4f440>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f61f4f440>
> .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: 0x558f61f4f440>
> 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: 0x558f62389670>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f62389670>
> .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: 0x558f62389670>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x558f62389670>
> .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: 0x558f62389670>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x558f62389670>
> .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: 0x558f62389670>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x558f62389670>
> .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: 0x558f62389670>
> 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: 0x558f63126390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x558f63126390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f63126390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f63126390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2197845100b4fd" "BufferedMatrixFile2197846f2931fa"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2197845100b4fd" "BufferedMatrixFile2197846f2931fa"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f632c6f50>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f632c6f50>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x558f632c6f50>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x558f632c6f50>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x558f632c6f50>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x558f632c6f50>
> .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: 0x558f632d1cb0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x558f632d1cb0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x558f632d1cb0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x558f632d1cb0>
> 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: 0x558f632d2570>
> .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: 0x558f632d2570>
> rm(P)
>
> proc.time()
user system elapsed
0.253 0.057 0.300
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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Platform: x86_64-pc-linux-gnu
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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
0.259 0.039 0.286