Habil Zare
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: RELEASE_3_7 |
| Last Commit: f0c7998 |
| Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:22 -0400 (Wed, 17 Oct 2018).
| Package 1097/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.6.0 Habil Zare
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Pigengene |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pigengene_1.6.0.tar.gz |
| StartedAt: 2018-10-17 03:59:11 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:10:04 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 653.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Pigengene.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pigengene_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:58: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:202: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/one.step.pigengene.Rd:154: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/wgcna.one.step.Rd:83: missing file link 'WGCNA-package'
See 'C:/Users/biocbuild/bbs-3.7-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.
':::' call which should be '::': 'C50:::as.party.C5.0'
See the note in ?`:::` about the use of this operator.
* 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")
check.pigengene.input: no visible global function definition for
'setNames'
welch.pvalue: no visible global function definition for 'as.formula'
welch.pvalue: no visible global function definition for 'oneway.test'
Undefined global functions or variables:
as.formula oneway.test setNames
Consider adding
importFrom("stats", "as.formula", "oneway.test", "setNames")
to your NAMESPACE file.
* 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 72.93 2.75 76.64
Pigengene-package 67.31 4.27 72.90
module.heatmap 21.25 0.59 21.84
compact.tree 19.41 0.14 19.63
make.decision.tree 18.19 0.18 18.38
compute.pigengene 9.24 0.31 9.62
wgcna.one.step 8.28 0.05 8.34
pigengene 6.77 0.67 7.44
plot.pigengene 6.61 0.47 7.08
learn.bn 6.00 0.04 6.92
project.eigen 4.94 0.31 5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Pigengene-package 54.96 2.03 60.56
one.step.pigengene 47.32 2.26 50.40
module.heatmap 17.48 0.47 18.19
make.decision.tree 13.56 0.12 13.69
compact.tree 12.80 0.04 13.69
wgcna.one.step 9.86 0.03 9.89
compute.pigengene 5.85 0.22 6.54
plot.pigengene 5.19 0.45 5.64
pigengene 4.84 0.41 5.29
learn.bn 4.47 0.05 5.53
* 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-3.7-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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Pigengene_1.6.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.6.0.zip && rm Pigengene_1.6.0.tar.gz Pigengene_1.6.0.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
100 2452k 100 2452k 0 0 29.6M 0 --:--:-- --:--:-- --:--:-- 32.3M
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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
aml html
balance html
calculate.beta html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
dcor.matrix html
draw.bn html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/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_1.6.0.zip
* DONE (Pigengene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-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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