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CHECK report for ramwas on tokay2

This page was generated on 2019-10-16 12:37:26 -0400 (Wed, 16 Oct 2019).

Package 1308/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.8.0
Andrey A Shabalin
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ramwas
Branch: RELEASE_3_9
Last Commit: 3841343
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ramwas
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ramwas.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ramwas_1.8.0.tar.gz
StartedAt: 2019-10-16 06:20:00 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:24:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 284.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ramwas.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ramwas.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ramwas_1.8.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ramwas.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ramwas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ramwas' version '1.8.0'
* 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
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ramwas/libs/i386/ramwas.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
manhattan 9.73   0.44   10.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
manhattan 8.86   0.61    9.47
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ramwas.Rcheck/00check.log'
for details.



Installation output

ramwas.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ramwas_1.8.0.tar.gz && rm -rf ramwas.buildbin-libdir && mkdir ramwas.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ramwas.buildbin-libdir ramwas_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ramwas_1.8.0.zip && rm ramwas_1.8.0.tar.gz ramwas_1.8.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  210k  100  210k    0     0  2991k      0 --:--:-- --:--:-- --:--:-- 3395k

install for i386

* installing *source* package 'ramwas' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rw_c_code.c -o rw_c_code.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ramwas.buildbin-libdir/00LOCK-ramwas/00new/ramwas/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ramwas'
    finding HTML links ... done
    MakeBED                                 html  
    QCs                                     html  
    RaMWAS                                  html  
    cachedRDSload                           html  
    findBestNpvs                            html  
    get                                     html  
    getCpGset                               html  
    injectSNPsMAF                           html  
    finding level-2 HTML links ... done

    insilicoFASTQ                           html  
    isAbsolutePath                          html  
    makefullpath                            html  
    manhattan                               html  
    mat2cols                                html  
    orthonormalizeCovariates                html  
    parameterDump                           html  
    parameterPreprocess                     html  
    parametersFromFile                      html  
    pipeline                                html  
    plotCV                                  html  
    plotFragmentSizeDistributionEstimate    html  
    plotPC                                  html  
    processCommandLine                      html  
    pvalue2qvalue                           html  
    qqplotFast                              html  
    ramwas0createArtificialData             html  
    ramwasAnnotateLocations                 html  
    ramwasParameters                        html  
    rowcolSumSq                             html  
    rwDataClass-class                       html  
    subsetData                              html  
    testPhenotype                           html  
*** 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

install for x64

* installing *source* package 'ramwas' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rw_c_code.c -o rw_c_code.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ramwas.buildbin-libdir/ramwas/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ramwas' as ramwas_1.8.0.zip
* DONE (ramwas)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ramwas' successfully unpacked and MD5 sums checked

Tests output


Example timings

ramwas.Rcheck/examples_i386/ramwas-Ex.timings

nameusersystemelapsed
MakeBED000
QCs0.050.011.84
cachedRDSload1.290.001.30
findBestNpvs000
get000
getCpGset3.800.173.97
injectSNPsMAF0.560.020.57
insilicoFASTQ000
isAbsolutePath000
makefullpath000
manhattan 9.73 0.4410.17
mat2cols000
orthonormalizeCovariates0.020.000.02
parameterDump000
parameterPreprocess0.010.000.01
parametersFromFile000
pipeline000
plotCV0.360.030.39
plotFragmentSizeDistributionEstimate0.020.000.60
plotPC000
processCommandLine000
pvalue2qvalue000
qqplotFast1.330.161.48
ramwas0createArtificialData0.370.010.39
ramwasAnnotateLocations000
ramwasParameters000
rowcolSumSq000
rwDataClass-class0.050.000.05
subsetData000
testPhenotype0.020.000.02

ramwas.Rcheck/examples_x64/ramwas-Ex.timings

nameusersystemelapsed
MakeBED000
QCs0.040.000.05
cachedRDSload1.250.001.25
findBestNpvs0.020.000.01
get000
getCpGset3.090.103.19
injectSNPsMAF0.660.010.67
insilicoFASTQ000
isAbsolutePath000
makefullpath000
manhattan8.860.619.47
mat2cols000
orthonormalizeCovariates0.010.000.02
parameterDump000
parameterPreprocess0.020.000.01
parametersFromFile000
pipeline000
plotCV0.340.020.36
plotFragmentSizeDistributionEstimate0.030.000.03
plotPC000
processCommandLine000
pvalue2qvalue0.020.000.02
qqplotFast0.720.160.87
ramwas0createArtificialData0.340.030.46
ramwasAnnotateLocations000
ramwasParameters000
rowcolSumSq000
rwDataClass-class0.070.000.06
subsetData000
testPhenotype0.030.000.03