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CHECK report for CancerMutationAnalysis on tokay1

This page was generated on 2020-08-06 11:54:27 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CancerMutationAnalysis PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 220/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerMutationAnalysis 1.31.0
Simina M. Boca
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/CancerMutationAnalysis
Branch: master
Last Commit: 251c81e
Last Changed Date: 2020-04-27 14:29:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerMutationAnalysis
Version: 1.31.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerMutationAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CancerMutationAnalysis_1.31.0.tar.gz
StartedAt: 2020-08-06 00:45:18 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 00:50:56 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 337.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CancerMutationAnalysis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CancerMutationAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CancerMutationAnalysis_1.31.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CancerMutationAnalysis.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CancerMutationAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CancerMutationAnalysis' version '1.31.0'
* 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 'CancerMutationAnalysis' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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 ... NOTE
Package in Depends field not imported from: 'qvalue'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ebfdr: no visible global function definition for 'density'
ebfdr: no visible global function definition for 'text'
ebfdr: no visible global function definition for 'abline'
ebfdr: no visible global function definition for 'rug'
ebfdr: no visible global function definition for 'hist'
p2q: no visible global function definition for 'qvalue'
perm.null.het.p.values: no visible global function definition for
  'dhyper'
perm.null.p.values: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  abline density dhyper hist qvalue rug text
Consider adding
  importFrom("graphics", "abline", "hist", "rug", "text")
  importFrom("stats", "density", "dhyper")
to your NAMESPACE file.
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CancerMutationAnalysis/libs/i386/CancerMutationAnalysis.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CancerMutationAnalysis/libs/x64/CancerMutationAnalysis.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 (user + system) or elapsed time > 5s
             user system elapsed
cma.set.sim 60.93   2.19   63.58
cma.fdr     37.17   4.87   42.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
cma.set.sim 51.55   2.74   54.28
cma.fdr     30.84   2.03   32.88
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CancerMutationAnalysis.Rcheck/00check.log'
for details.



Installation output

CancerMutationAnalysis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CancerMutationAnalysis_1.31.0.tar.gz && rm -rf CancerMutationAnalysis.buildbin-libdir && mkdir CancerMutationAnalysis.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CancerMutationAnalysis.buildbin-libdir CancerMutationAnalysis_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CancerMutationAnalysis_1.31.0.zip && rm CancerMutationAnalysis_1.31.0.tar.gz CancerMutationAnalysis_1.31.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 8104k  100 8104k    0     0  54.4M      0 --:--:-- --:--:-- --:--:-- 55.3M

install for i386

* installing *source* package 'CancerMutationAnalysis' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get.cdf.het.berns.c -o get.cdf.het.berns.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CancerMutationAnalysis.dll tmp.def get.cdf.het.berns.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CancerMutationAnalysis.buildbin-libdir/00LOCK-CancerMutationAnalysis/00new/CancerMutationAnalysis/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CancerMutationAnalysis'
    finding HTML links ... done
    BackRatesBreast                         html  
    BackRatesColon                          html  
    BackRatesGBM                            html  
    BackRatesMB                             html  
    BackRatesPancreas                       html  
    EntrezID2Name                           html  
    GeneAlterBreast                         html  
    GeneAlterColon                          html  
    GeneAlterGBM                            html  
    GeneAlterMB                             html  
    GeneAlterPancreas                       html  
    GeneCovBreast                           html  
    GeneCovColon                            html  
    GeneCovGBM                              html  
    GeneCovMB                               html  
    GeneCovPancreas                         html  
    GeneID2Name11                           html  
    GeneSampBreast                          html  
    GeneSampColon                           html  
    GeneSampGBM                             html  
    GeneSampMB                              html  
    GeneSampPancreas                        html  
    SetMethodsSims-class                    html  
    cma.fdr                                 html  
    cma.scores                              html  
    cma.set.sim                             html  
    cma.set.stat                            html  
    combine.sims                            html  
    extract.sims.method                     html  
** 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 'CancerMutationAnalysis' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c get.cdf.het.berns.c -o get.cdf.het.berns.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CancerMutationAnalysis.dll tmp.def get.cdf.het.berns.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CancerMutationAnalysis.buildbin-libdir/CancerMutationAnalysis/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CancerMutationAnalysis' as CancerMutationAnalysis_1.31.0.zip
* DONE (CancerMutationAnalysis)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CancerMutationAnalysis' successfully unpacked and MD5 sums checked

Tests output


Example timings

CancerMutationAnalysis.Rcheck/examples_i386/CancerMutationAnalysis-Ex.timings

nameusersystemelapsed
cma.fdr37.17 4.8742.04
cma.scores0.550.020.57
cma.set.sim60.93 2.1963.58
cma.set.stat4.950.045.00
combine.sims000
extract.sims.method000

CancerMutationAnalysis.Rcheck/examples_x64/CancerMutationAnalysis-Ex.timings

nameusersystemelapsed
cma.fdr30.84 2.0332.88
cma.scores0.490.030.52
cma.set.sim51.55 2.7454.28
cma.set.stat3.140.013.15
combine.sims000
extract.sims.method000