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This page was generated on 2024-03-04 11:39:14 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 793/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.29.0  (landing page)
Mathieu Emily
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/GeneGeneInteR
git_branch: devel
git_last_commit: 595ad4a
git_last_commit_date: 2023-10-24 10:51:41 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for GeneGeneInteR on merida1


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: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneGeneInteR_1.29.0.tar.gz
StartedAt: 2024-03-02 04:23:05 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 04:29:32 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 387.5 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/Resources/bin/R CMD check --install=check:GeneGeneInteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneGeneInteR_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneGeneInteR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneGeneInteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneGeneInteR’ version ‘1.29.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
GBIGM.test 5.919  0.084   6.867
PLSPM.test 4.914  0.079   6.084
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/GeneGeneInteR.Rcheck/00check.log’
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneGeneInteR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GeneGeneInteR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c chclust.cpp -o chclust.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GeneGeneInteR.so chclust.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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.test1.1730.0701.513
CLD.test2.3310.0313.041
GBIGM.test5.9190.0846.867
GGI1.8580.0422.336
KCCA.test0.0020.0030.004
PCA.test0.0750.0050.092
PLSPM.test4.9140.0796.084
gates.test0.5420.0120.661
importFile0.7020.0140.838
imputeSnpMatrix0.8560.0251.028
minP.test0.7640.0120.940
plot.GGInetwork0.1720.0120.216
print.GGItest0.0320.0040.039
selectSnps0.0090.0020.013
snpMatrixScour0.0540.0020.062
summary.GGInetwork0.0090.0030.013
summary.GGItest0.0330.0030.039
tProd.test0.6490.0130.773
tTS.test0.6630.0160.769