Habil Zare
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/Pigengene |
| Branch: master |
| Last Commit: aac85cf |
| Last Changed Date: 2020-01-04 01:25:16 -0500 (Sat, 04 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:45:22 -0500 (Thu, 16 Jan 2020).
| Package 1265/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Pigengene 1.13.6 Habil Zare
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | OK | ERROR | ERROR | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Pigengene |
| Version: 1.13.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.13.6.tar.gz |
| StartedAt: 2020-01-16 07:28:24 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:39:49 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 685.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.13.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.13.6’
* 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 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")
combine.networks: no visible binding for global variable ‘netwok’
Undefined global functions or variables:
netwok
* 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 ... NOTE
Output for data("pigengene", package = "Pigengene"):
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
one.step.pigengene 104.830 7.006 111.793
Pigengene-package 102.232 7.409 109.520
module.heatmap 31.688 3.917 36.041
compact.tree 21.367 3.482 24.929
make.decision.tree 21.704 3.142 24.875
plot.pigengene 15.235 1.551 16.705
learn.bn 16.347 0.249 16.566
compute.pigengene 13.465 1.303 14.780
project.eigen 13.388 1.380 14.743
pigengene 12.136 1.401 13.540
combine.networks 11.662 0.170 11.857
wgcna.one.step 10.498 0.096 10.585
gene.mapping 9.034 0.932 15.405
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)
Pigengene.Rcheck/Pigengene-Ex.timings
| name | user | system | elapsed | |
| Pigengene-package | 102.232 | 7.409 | 109.520 | |
| aml | 0.455 | 0.048 | 0.484 | |
| balance | 3.233 | 0.272 | 3.507 | |
| calculate.beta | 0.890 | 0.128 | 1.019 | |
| check.nas | 0.071 | 0.019 | 0.090 | |
| check.pigengene.input | 0.063 | 0.015 | 0.079 | |
| combine.networks | 11.662 | 0.170 | 11.857 | |
| compact.tree | 21.367 | 3.482 | 24.929 | |
| compute.pigengene | 13.465 | 1.303 | 14.780 | |
| dcor.matrix | 0.310 | 0.133 | 0.445 | |
| draw.bn | 0 | 0 | 0 | |
| eigengenes33 | 0.178 | 0.008 | 0.186 | |
| gene.mapping | 9.034 | 0.932 | 15.405 | |
| get.fitted.leaf | 1.048 | 0.135 | 1.166 | |
| get.genes | 1.035 | 0.112 | 1.152 | |
| get.used.features | 1.146 | 0.105 | 1.256 | |
| learn.bn | 16.347 | 0.249 | 16.566 | |
| make.decision.tree | 21.704 | 3.142 | 24.875 | |
| mds | 0.170 | 0.014 | 0.185 | |
| message.if | 0.000 | 0.000 | 0.001 | |
| module.heatmap | 31.688 | 3.917 | 36.041 | |
| one.step.pigengene | 104.830 | 7.006 | 111.793 | |
| pheatmap.type | 0.977 | 0.033 | 1.016 | |
| pigengene | 12.136 | 1.401 | 13.540 | |
| plot.pigengene | 15.235 | 1.551 | 16.705 | |
| preds.at | 1.219 | 0.161 | 1.382 | |
| project.eigen | 13.388 | 1.380 | 14.743 | |
| pvalues.manova | 0.152 | 0.023 | 0.169 | |
| save.if | 0.626 | 0.037 | 0.663 | |
| wgcna.one.step | 10.498 | 0.096 | 10.585 | |