Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for Pigengene on veracruz2

This page was generated on 2017-10-18 14:34:40 -0400 (Wed, 18 Oct 2017).

Package 984/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.2.0
Habil Zare
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_5
Last Commit: 12a139e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Pigengene
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz
StartedAt: 2017-10-18 07:18:02 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:24:43 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 401.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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")

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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Pigengene-package  63.725  2.745  68.462
one.step.pigengene 60.858  2.795  65.664
module.heatmap     25.369  1.508  28.721
make.decision.tree 15.456  0.980  16.964
compact.tree       14.840  0.902  16.181
compute.pigengene   9.149  0.581  10.005
plot.pigengene      8.595  0.647   9.571
project.eigen       6.870  0.618   7.752
wgcna.one.step      7.362  0.106   7.717
pigengene           5.892  0.561   6.688
learn.bn            5.710  0.096   6.116
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck/00check.log’
for details.


Pigengene.Rcheck/00install.out:

* installing *source* package ‘Pigengene’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Pigengene)

Pigengene.Rcheck/Pigengene-Ex.timings:

nameusersystemelapsed
Pigengene-package63.725 2.74568.462
aml0.1600.0060.169
balance0.9450.1441.111
calculate.beta2.6050.0342.696
check.pigengene.input0.0450.0050.050
compact.tree14.840 0.90216.181
compute.pigengene 9.149 0.58110.005
dcor.matrix0.2240.0450.280
draw.bn0.0010.0000.001
eigengenes330.1310.0030.138
gene.mapping1.8660.1082.022
get.fitted.leaf0.8980.0560.975
get.genes0.8460.0520.916
get.used.features0.7920.0470.945
learn.bn5.7100.0966.116
make.decision.tree15.456 0.98016.964
mds0.1400.0070.153
module.heatmap25.369 1.50828.721
one.step.pigengene60.858 2.79565.664
pheatmap.type0.2300.0050.243
pigengene5.8920.5616.688
plot.pigengene8.5950.6479.571
preds.at0.9520.0731.050
project.eigen6.8700.6187.752
pvalues.manova0.0310.0010.033
wgcna.one.step7.3620.1067.717