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This page was generated on 2023-10-16 11:35:37 -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 1521/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.26.0  (landing page)
Habil Zare
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: RELEASE_3_17
git_last_commit: ed5b2c2
git_last_commit_date: 2023-04-25 10:47:16 -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 Pigengene on nebbiolo1


To the developers/maintainers of the Pigengene package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.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: Pigengene
Version: 1.26.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pigengene_1.26.0.tar.gz
StartedAt: 2023-10-15 23:54:10 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-16 00:06:37 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 747.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pigengene_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Pigengene’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘Pigengene/R/bn.calculation.R’:
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

compute.pigengene: no visible global function definition for ‘prcomp’
one.step.pigengene: no visible binding for global variable
  ‘org.Hs.eg.db’
Undefined global functions or variables:
  org.Hs.eg.db prcomp
Consider adding
  importFrom("stats", "prcomp")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) get.enriched.pw.Rd:71: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
Pigengene-package  71.748  1.567  73.232
one.step.pigengene 71.517  0.793  72.313
get.enriched.pw    62.860  3.797  66.686
module.heatmap     34.689  0.420  35.098
learn.bn           15.541  0.092  15.633
make.filter        14.508  0.132  14.640
apply.filter       14.140  0.200  14.341
combine.networks   13.487  0.068  13.535
determine.modules  13.339  0.140  13.479
wgcna.one.step     11.466  0.016  11.481
compact.tree        9.973  0.060  10.033
make.decision.tree  9.726  0.080   9.806
pigengene           6.023  0.112   6.135
plot.pigengene      5.792  0.044   5.836
compute.pigengene   5.674  0.076   5.750
gene.mapping        5.051  0.460  16.274
project.eigen       5.416  0.032   5.449
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Pigengene_inference.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘Pigengene’ ...
** using staged installation
** R
** data
** 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 (Pigengene)

Tests output


Example timings

Pigengene.Rcheck/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package71.748 1.56773.232
aml0.1690.0140.167
apply.filter14.140 0.20014.341
balance0.3570.0960.453
calculate.beta0.6850.0080.694
check.nas0.0400.0030.043
check.pigengene.input0.0430.0000.043
combine.networks13.487 0.06813.535
compact.tree 9.973 0.06010.033
compute.pigengene5.6740.0765.750
dcor.matrix0.1250.0000.125
determine.modules13.339 0.14013.479
draw.bn000
eigengenes330.0790.0000.079
gene.mapping 5.051 0.46016.274
get.enriched.pw62.860 3.79766.686
get.fitted.leaf1.4870.0381.525
get.genes0.4810.0160.496
get.used.features0.4740.0200.494
learn.bn15.541 0.09215.633
make.decision.tree9.7260.0809.806
make.filter14.508 0.13214.640
mds0.0830.0080.091
message.if0.0000.0000.001
module.heatmap34.689 0.42035.098
one.step.pigengene71.517 0.79372.313
pheatmap.type0.1950.0040.198
pigengene6.0230.1126.135
plot.pigengene5.7920.0445.836
preds.at0.5670.0120.579
project.eigen5.4160.0325.449
pvalues.manova0.0630.0040.067
save.if0.7070.0040.711
wgcna.one.step11.466 0.01611.481