Kristian K Ullrich
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MSA2dist |
| git_branch: master |
| git_last_commit: a7cdd79 |
| git_last_commit_date: 2022-01-27 15:21:52 -0400 (Thu, 27 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:05 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the MSA2dist package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSA2dist.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1217/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSA2dist 0.99.2 (landing page) Kristian K Ullrich
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MSA2dist |
| Version: 0.99.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSA2dist.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSA2dist_0.99.2.tar.gz |
| StartedAt: 2022-03-17 19:39:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:42:26 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 162.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSA2dist.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSA2dist.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSA2dist_0.99.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MSA2dist.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSA2dist/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSA2dist' version '0.99.2'
* package encoding: UTF-8
* 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 whether package 'MSA2dist' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
See 'D:/biocbuild/bbs-3.15-bioc/meat/MSA2dist.Rcheck/00install.out' for details.
* 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 R 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/MSA2dist/libs/x64/MSA2dist.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
codonmat2xy 0.55 0.04 11.59
dnastring2kaks 0.23 0.02 8.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/MSA2dist.Rcheck/00check.log'
for details.
MSA2dist.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MSA2dist
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MSA2dist' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rcpp_distSTRING.cpp -o rcpp_distSTRING.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppThread/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MSA2dist.dll tmp.def RcppExports.o rcpp_distSTRING.o rcpp_pairwiseDeletionAA.o rcpp_pairwiseDeletionDNA.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MSA2dist/00new/MSA2dist/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** help
*** installing help indices
converting help for package 'MSA2dist'
finding HTML links ... done
AAMatrix-data html
GENETIC_CODE_TCAG html
aabin2aastring html
aastring2aabin html
aastring2aln html
aastring2dist html
addmask2string html
addpop2string html
addpos2string html
addregion2string html
aln2aastring html
aln2dnastring html
cds2aa html
codon2numberAMBIG html
codon2numberTCAG html
codonmat2pnps html
codonmat2xy html
compareCodons html
dnabin2dnastring html
dnastring2aln html
dnastring2codonmat html
dnastring2dist html
dnastring2dnabin html
dnastring2kaks html
getmask html
getpos html
globalDeletion html
granthamMatrix html
hiv-data html
iupac-data html
iupacMatrix html
popinteger html
popnames html
rcpp_distSTRING html
rcpp_pairwiseDeletionAA html
rcpp_pairwiseDeletionDNA html
region html
regionused html
string2region html
subString html
uptriidx html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** testing if installed package keeps a record of temporary installation path
* DONE (MSA2dist)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'npGSEA' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'transcriptogramer' is missing or broken
done
MSA2dist.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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(testthat)
> library(MSA2dist)
Warning message:
replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
>
> test_check("MSA2dist")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 69 ]
>
> proc.time()
user system elapsed
7.93 0.78 27.54
MSA2dist.Rcheck/MSA2dist-Ex.timings
| name | user | system | elapsed | |
| AAMatrix-data | 0 | 0 | 0 | |
| GENETIC_CODE_TCAG | 0 | 0 | 0 | |
| aabin2aastring | 0.03 | 0.00 | 0.03 | |
| aastring2aabin | 0.22 | 0.00 | 0.22 | |
| aastring2aln | 0.14 | 0.00 | 0.14 | |
| aastring2dist | 0.69 | 0.03 | 0.69 | |
| addmask2string | 0.15 | 0.03 | 0.18 | |
| addpop2string | 0.16 | 0.03 | 0.19 | |
| addpos2string | 0.16 | 0.02 | 0.17 | |
| addregion2string | 0.17 | 0.01 | 0.19 | |
| aln2aastring | 0.14 | 0.00 | 0.14 | |
| aln2dnastring | 0.02 | 0.00 | 0.02 | |
| cds2aa | 0.4 | 0.0 | 0.4 | |
| codon2numberAMBIG | 0 | 0 | 0 | |
| codon2numberTCAG | 0 | 0 | 0 | |
| codonmat2pnps | 0.03 | 0.02 | 0.05 | |
| codonmat2xy | 0.55 | 0.04 | 11.59 | |
| compareCodons | 0.03 | 0.00 | 0.03 | |
| dnabin2dnastring | 0.03 | 0.00 | 0.04 | |
| dnastring2aln | 0 | 0 | 0 | |
| dnastring2codonmat | 0.03 | 0.00 | 0.03 | |
| dnastring2dist | 0.16 | 0.00 | 0.16 | |
| dnastring2dnabin | 0 | 0 | 0 | |
| dnastring2kaks | 0.23 | 0.02 | 8.81 | |
| getmask | 0.21 | 0.00 | 0.20 | |
| getpos | 0.09 | 0.01 | 0.11 | |
| globalDeletion | 0.02 | 0.00 | 0.02 | |
| granthamMatrix | 0 | 0 | 0 | |
| hiv-data | 0.04 | 0.00 | 0.05 | |
| iupac-data | 0.05 | 0.03 | 0.07 | |
| iupacMatrix | 0 | 0 | 0 | |
| popinteger | 0.58 | 0.03 | 0.61 | |
| popnames | 0.25 | 0.00 | 0.25 | |
| rcpp_distSTRING | 0.03 | 0.00 | 0.03 | |
| rcpp_pairwiseDeletionAA | 0.20 | 0.04 | 0.24 | |
| rcpp_pairwiseDeletionDNA | 0.02 | 0.00 | 0.01 | |
| region | 0.25 | 0.00 | 0.25 | |
| regionused | 0.19 | 0.03 | 0.22 | |
| string2region | 0.56 | 0.01 | 0.58 | |
| subString | 0.01 | 0.00 | 0.02 | |
| uptriidx | 0 | 0 | 0 | |