Habil Zare
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/Pigengene |
| git_branch: RELEASE_3_14 |
| git_last_commit: 91cef1f |
| git_last_commit_date: 2021-10-26 12:28:05 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:05 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the Pigengene package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1420/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pigengene 1.20.0 (landing page) Habil Zare
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: Pigengene |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pigengene_1.20.0.tar.gz |
| StartedAt: 2022-04-13 00:33:26 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 00:49:35 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 968.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pigengene_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pigengene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pigengene' version '1.20.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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.
Package in Depends field not imported from: 'BiocStyle'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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")
apply.filter: no visible binding for global variable 'epsilon'
get.enriched.pw: no visible global function definition for 'enrichNCG'
one.step.pigengene: no visible binding for global variable
'org.Hs.eg.db'
Undefined global functions or variables:
enrichNCG epsilon org.Hs.eg.db
* checking Rd files ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Pigengene-package 68.44 3.49 72.97
one.step.pigengene 64.17 2.60 67.71
module.heatmap 40.28 4.54 45.04
gene.mapping 29.43 1.14 36.09
learn.bn 16.28 0.06 17.06
compact.tree 14.50 0.08 14.58
make.decision.tree 13.00 0.27 13.27
combine.networks 11.53 0.00 11.63
wgcna.one.step 10.00 0.03 10.04
pigengene 6.95 0.48 7.44
compute.pigengene 6.31 0.41 6.72
plot.pigengene 6.01 0.36 6.38
project.eigen 5.75 0.29 6.04
get.enriched.pw 1.53 0.18 6.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
one.step.pigengene 69.70 2.55 91.35
Pigengene-package 68.65 1.88 71.73
module.heatmap 39.72 4.67 53.03
gene.mapping 19.40 0.56 22.82
learn.bn 17.28 0.06 18.53
make.decision.tree 14.55 0.11 14.67
compact.tree 13.17 0.19 13.36
combine.networks 12.66 0.02 12.71
wgcna.one.step 10.33 0.00 10.33
compute.pigengene 6.56 0.40 7.05
pigengene 6.21 0.36 6.84
plot.pigengene 5.36 0.32 5.67
project.eigen 4.89 0.17 5.09
get.enriched.pw 1.63 0.20 6.79
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck/00check.log'
for details.
Pigengene.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Pigengene_1.20.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.20.0.zip && rm Pigengene_1.20.0.tar.gz Pigengene_1.20.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
52 2474k 52 1291k 0 0 1508k 0 0:00:01 --:--:-- 0:00:01 1507k
100 2474k 100 2474k 0 0 1622k 0 0:00:01 0:00:01 --:--:-- 1623k
install for i386
* installing *source* package 'Pigengene' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Pigengene'
finding HTML links ... done
Pigengene-package html
aml html
balance html
calculate.beta html
check.nas html
check.pigengene.input html
combine.networks html
compact.tree html
compute.pigengene html
dcor.matrix html
draw.bn html
eigengenes33 html
gene.mapping html
get.enriched.pw html
get.fitted.leaf html
get.genes html
get.used.features html
learn.bn html
make.decision.tree html
mds html
message.if html
module.heatmap html
one.step.pigengene html
pheatmap.type html
pigengene-class html
pigengene html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.buildbin-libdir/00LOCK-Pigengene/00new/Pigengene/help/pigengene.html
plot.pigengene html
preds.at html
project.eigen html
pvalues.manova html
save.if html
wgcna.one.step html
** 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
install for x64
* installing *source* package 'Pigengene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pigengene' as Pigengene_1.20.0.zip
* DONE (Pigengene)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked
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Pigengene.Rcheck/examples_i386/Pigengene-Ex.timings
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Pigengene.Rcheck/examples_x64/Pigengene-Ex.timings
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