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This page was generated on 2021-09-17 15:05:41 -0400 (Fri, 17 Sep 2021).

CHECK results for GeneGeneInteR on nebbiolo1

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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.18.0.tar.gz
StartedAt: 2021-09-16 09:55:56 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 09:58:29 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 153.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneGeneInteR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneGeneInteR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 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 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 is not available
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GeneGeneInteR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘GeneGeneInteR’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c chclust.cpp -o chclust.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o GeneGeneInteR.so chclust.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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.test1.4620.0281.490
CLD.test0.8550.0080.863
GBIGM.test2.5760.0442.620
GGI0.8940.0200.916
KCCA.test0.0010.0000.001
PCA.test0.030.000.03
PLSPM.test2.3490.0202.369
gates.test0.2340.0000.234
importFile0.2720.0040.280
imputeSnpMatrix0.5470.0070.555
minP.test0.3540.0090.362
plot.GGInetwork0.0780.0000.079
print.GGItest0.0160.0000.016
selectSnps0.0050.0000.005
snpMatrixScour0.0230.0030.027
summary.GGInetwork0.0050.0010.004
summary.GGItest0.0160.0000.016
tProd.test0.2660.0030.269
tTS.test0.2780.0010.278