Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:32 -0400 (Sat, 17 Oct 2020).
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 682/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GeneGeneInteR 1.14.0 Mathieu Emily
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: GeneGeneInteR |
Version: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2020-10-17 01:25:41 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:35:00 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 559.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneGeneInteR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneGeneInteR.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.14.0’ * 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-3.11-bioc/meat/GeneGeneInteR.Rcheck/00check.log’ for details.
GeneGeneInteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneGeneInteR ### ############################################################################## ############################################################################## * 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)
GeneGeneInteR.Rcheck/GeneGeneInteR-Ex.timings
name | user | system | elapsed | |
CCA.test | 0.962 | 0.073 | 1.040 | |
CLD.test | 1.431 | 0.063 | 1.495 | |
GBIGM.test | 4.446 | 0.066 | 4.516 | |
GGI | 1.654 | 0.050 | 1.706 | |
KCCA.test | 0.000 | 0.000 | 0.002 | |
PCA.test | 0.041 | 0.003 | 0.044 | |
PLSPM.test | 0.033 | 0.004 | 0.037 | |
gates.test | 0.495 | 0.029 | 0.523 | |
importFile | 0.621 | 0.015 | 0.637 | |
imputeSnpMatrix | 0.877 | 0.017 | 0.896 | |
minP.test | 1.684 | 0.014 | 1.700 | |
plot.GGInetwork | 0.134 | 0.008 | 0.143 | |
print.GGItest | 0.024 | 0.002 | 0.026 | |
selectSnps | 0.008 | 0.001 | 0.009 | |
snpMatrixScour | 0.051 | 0.002 | 0.052 | |
summary.GGInetwork | 0.008 | 0.002 | 0.009 | |
summary.GGItest | 0.031 | 0.003 | 0.034 | |
tProd.test | 0.448 | 0.019 | 0.466 | |
tTS.test | 0.526 | 0.015 | 0.541 | |