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This page was generated on 2021-09-17 15:06:06 -0400 (Fri, 17 Sep 2021).

CHECK results for GeneGeneInteR on tokay2

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

raw results

Package 716/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.18.0  (landing page)
Mathieu Emily
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneGeneInteR
git_branch: RELEASE_3_13
git_last_commit: c3d7539
git_last_commit_date: 2021-05-19 12:21:57 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneGeneInteR
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneGeneInteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.18.0.tar.gz
StartedAt: 2021-09-16 23:31:07 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 23:35:05 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 238.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneGeneInteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneGeneInteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneGeneInteR' version '1.18.0'
* 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 'GeneGeneInteR' 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 ... NOTE
get_PLSR: no visible global function definition for 'cor'
get_PLSR_NA: no visible global function definition for 'cor'
get_boot_stats: no visible binding for global variable 'sd'
get_boots: no visible global function definition for 'cor'
get_num_scale: no visible global function definition for 'na.omit'
get_path_scheme: no visible global function definition for 'lm'
get_path_scheme: no visible global function definition for 'cor'
get_paths: no visible global function definition for 'lm'
get_scores: no visible global function definition for 'cor'
get_treated_data: no visible binding for global variable 'sd'
get_unidim: no visible binding for global variable 'sd'
get_unidim: no visible global function definition for 'princomp'
get_unidim: no visible global function definition for 'cor'
get_weights: no visible binding for global variable 'sd'
get_weights: no visible global function definition for 'cor'
get_weights_nonmetric: no visible binding for global variable
  'normalize'
get_weights_nonmetric: no visible global function definition for 'cor'
get_weights_nonmetric: no visible global function definition for 'lm'
get_weights_nonmetric: no visible binding for global variable 'sd'
plspm: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm na.omit normalize princomp sd
Consider adding
  importFrom("stats", "cor", "lm", "na.omit", "princomp", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown packages 'plspm', 'GGtools' in Rd xrefs
* 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 LazyData ... 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-3.13-bioc/R/library/GeneGeneInteR/libs/i386/GeneGeneInteR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GeneGeneInteR/libs/x64/GeneGeneInteR.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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.Rcheck/00check.log'
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneGeneInteR_1.18.0.tar.gz && rm -rf GeneGeneInteR.buildbin-libdir && mkdir GeneGeneInteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneGeneInteR_1.18.0.zip && rm GeneGeneInteR_1.18.0.tar.gz GeneGeneInteR_1.18.0.zip
###
##############################################################################
##############################################################################


  % 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  492k  100  492k    0     0  1183k      0 --:--:-- --:--:-- --:--:-- 1186k

install for i386

* installing *source* package 'GeneGeneInteR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chclust.cpp -o chclust.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GeneGeneInteR.dll tmp.def chclust.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.buildbin-libdir/00LOCK-GeneGeneInteR/00new/GeneGeneInteR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneGeneInteR'
    finding HTML links ... done
    CCA.test                                html  
    CLD.test                                html  
    GBIGM.test                              html  
    GGI                                     html  
    KCCA.test                               html  
    PCA.test                                html  
    PLSPM.test                              html  
    data.SNP                                html  
    gates.test                              html  
    gene.pair                               html  
    importFile                              html  
    imputeSnpMatrix                         html  
    minP.test                               html  
    plot.GGInetwork                         html  
    print.GGItest                           html  
    selectSnps                              html  
    snpMatrixScour                          html  
    summary.GGInetwork                      html  
    summary.GGItest                         html  
    tProd.test                              html  
    tTS.test                                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 'GeneGeneInteR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chclust.cpp -o chclust.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GeneGeneInteR.dll tmp.def chclust.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.buildbin-libdir/GeneGeneInteR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneGeneInteR' as GeneGeneInteR_1.18.0.zip
* DONE (GeneGeneInteR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GeneGeneInteR' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneGeneInteR.Rcheck/examples_i386/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test0.570.080.65
CLD.test1.360.011.38
GBIGM.test2.830.002.83
GGI1.270.101.53
KCCA.test000
PCA.test0.040.000.04
PLSPM.test2.440.002.44
gates.test0.270.030.30
importFile0.560.001.03
imputeSnpMatrix0.810.000.86
minP.test0.690.000.69
plot.GGInetwork0.090.000.10
print.GGItest0.030.000.03
selectSnps0.000.000.17
snpMatrixScour0.080.000.08
summary.GGInetwork000
summary.GGItest0.030.000.03
tProd.test0.450.030.48
tTS.test0.390.000.39

GeneGeneInteR.Rcheck/examples_x64/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test1.080.021.09
CLD.test0.960.000.97
GBIGM.test2.620.062.69
GGI1.000.001.02
KCCA.test000
PCA.test0.070.010.08
PLSPM.test2.430.002.43
gates.test0.320.000.35
importFile0.530.000.53
imputeSnpMatrix0.760.000.83
minP.test0.660.000.65
plot.GGInetwork0.140.000.14
print.GGItest0.030.000.03
selectSnps000
snpMatrixScour0.060.000.06
summary.GGInetwork0.020.000.02
summary.GGItest0.030.000.03
tProd.test0.450.000.45
tTS.test0.380.020.39