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This page was generated on 2023-10-16 11:36:10 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 780/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.26.0  (landing page)
Mathieu Emily
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GeneGeneInteR
git_branch: RELEASE_3_17
git_last_commit: df80f33
git_last_commit_date: 2023-04-25 10:48:27 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for GeneGeneInteR on palomino3


To the developers/maintainers of the GeneGeneInteR package:
- 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 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: GeneGeneInteR
Version: 1.26.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneGeneInteR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.26.0.tar.gz
StartedAt: 2023-10-16 02:26:06 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 02:28:54 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 167.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneGeneInteR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.26.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GeneGeneInteR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneGeneInteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneGeneInteR' 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 'GeneGeneInteR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 ... 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
Package unavailable to check Rd xrefs: 'plspm'
Unknown package '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 x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/GeneGeneInteR/libs/x64/GeneGeneInteR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... 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
  'F:/biocbuild/bbs-3.17-bioc/meat/GeneGeneInteR.Rcheck/00check.log'
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GeneGeneInteR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GeneGeneInteR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chclust.cpp -o chclust.o
g++ -std=gnu++17 -shared -s -static-libgcc -o GeneGeneInteR.dll tmp.def chclust.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GeneGeneInteR/00new/GeneGeneInteR/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (GeneGeneInteR)

Tests output


Example timings

GeneGeneInteR.Rcheck/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test0.520.030.55
CLD.test0.90.00.9
GBIGM.test2.300.022.31
GGI1.010.001.03
KCCA.test000
PCA.test0.030.000.03
PLSPM.test2.030.032.06
gates.test0.320.000.36
importFile0.260.000.83
imputeSnpMatrix0.470.000.48
minP.test0.970.000.97
plot.GGInetwork0.080.000.14
print.GGItest0.010.000.02
selectSnps0.020.000.03
snpMatrixScour0.030.000.03
summary.GGInetwork000
summary.GGItest0.020.000.02
tProd.test0.280.020.29
tTS.test0.280.000.28