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CHECK report for GeneGeneInteR on merida1

This page was generated on 2021-05-06 12:35:04 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GeneGeneInteR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 690/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.16.0  (landing page)
Mathieu Emily
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GeneGeneInteR
Branch: RELEASE_3_12
Last Commit: b8a4049
Last Changed Date: 2020-10-27 11:16:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GeneGeneInteR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneGeneInteR_1.16.0.tar.gz
StartedAt: 2021-05-06 02:01:34 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:09:50 -0400 (Thu, 06 May 2021)
EllapsedTime: 496.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneGeneInteR_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneGeneInteR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneGeneInteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneGeneInteR’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... 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
* 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 package ‘plspm’ 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 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 is not available
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneGeneInteR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneGeneInteR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c chclust.cpp -o chclust.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GeneGeneInteR.so chclust.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GeneGeneInteR/00new/GeneGeneInteR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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.test0.7900.0630.855
CLD.test1.2290.0591.290
GBIGM.test3.6730.0893.767
GGI1.4500.0281.520
KCCA.test0.0000.0000.002
PCA.test0.0470.0020.048
PLSPM.test2.9710.0333.009
gates.test0.4090.0130.427
importFile0.4970.0170.518
imputeSnpMatrix0.7100.0130.724
minP.test0.5460.0120.559
plot.GGInetwork0.1170.0080.125
print.GGItest0.0230.0020.025
selectSnps0.0080.0010.009
snpMatrixScour0.0360.0010.037
summary.GGInetwork0.0060.0010.006
summary.GGItest0.0250.0020.027
tProd.test0.4320.0060.438
tTS.test0.4730.0070.481