Habil Zare
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_8 |
| Last Commit: 59ee84d |
| Last Changed Date: 2019-01-04 13:06:36 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:45 -0400 (Sat, 13 Apr 2019).
| Package 1160/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.8.1 Habil Zare
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Pigengene |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Pigengene_1.8.1.tar.gz |
| StartedAt: 2019-04-13 04:33:32 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:43:28 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 595.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Pigengene.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Pigengene_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Pigengene.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/calculate.beta.Rd:58: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/draw.bn.Rd:18: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/draw.bn.Rd:67: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/gene.mapping.Rd:60: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/gene.mapping.Rd:61: file link 'org.Mm.eg.db' in package 'org.Mm.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:99: file link 'discretize' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:104: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:177: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:202: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/one.step.pigengene.Rd:154: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/wgcna.one.step.Rd:83: missing file link 'WGCNA-package'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Pigengene.Rcheck/00install.out' for details.
* 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.
* 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")
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Pigengene-package.Rd':
'[WGCNA]{WGCNA-package}'
Missing link or links in documentation object 'calculate.beta.Rd':
'[WGCNA]{WGCNA-package}'
Missing link or links in documentation object 'compute.pigengene.Rd':
'[WGCNA]{WGCNA-package}'
Missing link or links in documentation object 'learn.bn.Rd':
'[WGCNA]{WGCNA-package}'
Missing link or links in documentation object 'one.step.pigengene.Rd':
'[WGCNA]{WGCNA-package}'
Missing link or links in documentation object 'wgcna.one.step.Rd':
'[WGCNA]{WGCNA-package}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 or elapsed time > 5s
user system elapsed
one.step.pigengene 51.95 2.36 55.45
Pigengene-package 47.42 3.47 52.37
module.heatmap 16.72 0.56 17.28
make.decision.tree 12.91 0.08 12.98
compact.tree 12.57 0.25 12.97
wgcna.one.step 7.18 0.03 7.20
plot.pigengene 6.19 0.43 6.61
pigengene 6.03 0.36 6.39
compute.pigengene 5.15 0.39 5.65
project.eigen 4.98 0.27 5.25
learn.bn 4.56 0.06 5.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
one.step.pigengene 47.03 2.53 50.64
Pigengene-package 46.16 1.69 48.85
module.heatmap 16.88 0.53 17.42
make.decision.tree 12.83 0.08 12.91
compact.tree 12.30 0.03 12.88
wgcna.one.step 8.17 0.08 8.27
plot.pigengene 5.63 0.42 6.05
pigengene 5.59 0.37 5.96
project.eigen 4.75 0.28 5.03
compute.pigengene 4.68 0.33 5.01
* 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/Pigengene.Rcheck/00check.log'
for details.
Pigengene.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Pigengene_1.8.1.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.8.1.zip && rm Pigengene_1.8.1.tar.gz Pigengene_1.8.1.zip
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install for i386
* installing *source* package 'Pigengene' ...
** 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
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
aml html
balance html
calculate.beta html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/calculate.beta.Rd:58: missing file link 'WGCNA-package'
check.nas html
check.pigengene.input html
compact.tree html
compute.pigengene html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
dcor.matrix html
draw.bn html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/draw.bn.Rd:18: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/draw.bn.Rd:67: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
eigengenes33 html
gene.mapping html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/gene.mapping.Rd:60: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/gene.mapping.Rd:61: file link 'org.Mm.eg.db' in package 'org.Mm.eg.db' does not exist and so has been treated as a topic
get.fitted.leaf html
get.genes html
get.used.features html
learn.bn html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:99: file link 'discretize' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:104: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:177: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/learn.bn.Rd:202: missing file link 'WGCNA-package'
make.decision.tree html
mds html
module.heatmap html
one.step.pigengene html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/one.step.pigengene.Rd:154: missing file link 'WGCNA-package'
pheatmap.type html
pigengene-class html
pigengene html
plot.pigengene html
preds.at html
project.eigen html
pvalues.manova html
wgcna.one.step html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmaunpv/R.INSTALLe445d3923ca/Pigengene/man/wgcna.one.step.Rd:83: missing file link 'WGCNA-package'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Pigengene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pigengene' as Pigengene_1.8.1.zip
* DONE (Pigengene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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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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