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This page was generated on 2024-04-17 11:37:10 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1654/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.26.0  (landing page)
Andrey A Shabalin
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/ramwas
git_branch: RELEASE_3_18
git_last_commit: cb4c072
git_last_commit_date: 2023-10-24 10:54:39 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ramwas on palomino4


To the developers/maintainers of the ramwas package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ramwas.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.

raw results


Summary

Package: ramwas
Version: 1.26.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ramwas.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ramwas_1.26.0.tar.gz
StartedAt: 2024-04-16 04:06:29 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:11:14 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 285.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ramwas.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ramwas_1.26.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ramwas.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ramwas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ramwas' version '1.26.0'
* 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 whether package 'ramwas' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/ramwas/libs/x64/ramwas.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 nor [v]sprintf. 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
manhattan  8.5   0.19    8.68
* 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 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/ramwas.Rcheck/00check.log'
for details.



Installation output

ramwas.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ramwas
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'ramwas' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rw_c_code.c -o rw_c_code.o
gcc -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-ramwas/00new/ramwas/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ramwas)

Tests output


Example timings

ramwas.Rcheck/ramwas-Ex.timings

nameusersystemelapsed
MakeBED000
QCs0.030.020.05
cachedRDSload1.720.001.71
findBestNpvs000
get000
getCpGset3.340.173.83
injectSNPsMAF0.990.000.99
insilicoFASTQ000
isAbsolutePath000
makefullpath000
manhattan8.500.198.68
mat2cols000
orthonormalizeCovariates0.010.000.02
parameterDump0.000.000.02
parameterPreprocess000
parametersFromFile0.000.000.01
pipeline000
plotCV1.800.011.81
plotFragmentSizeDistributionEstimate0.010.000.02
plotPC0.020.000.01
processCommandLine000
pvalue2qvalue000
qqplotFast1.620.101.72
ramwas0createArtificialData0.330.000.41
ramwasAnnotateLocations000
ramwasParameters000
rowcolSumSq000
rwDataClass-class0.020.000.01
subsetData000
testPhenotype0.010.000.02