BioC 3.3: CHECK report for gCMAP on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:14 -0400 (Tue, 27 Oct 2015).
gCMAP 1.15.0 Thomas Sandmann
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gCMAP | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
Summary
Package: gCMAP |
Version: 1.15.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz |
StartedAt: 2015-10-27 04:01:19 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 04:04:29 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 190.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gCMAP.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCMAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCMAP’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘bigmemoryExtras’
* 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 ‘gCMAP’ can be installed ... [20s/20s] 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:
‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
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
camera_score,eSet-CMAPCollection: no visible global function definition
for ‘camera’
induceCMAPCollection,eSet : <anonymous>: no visible global function
definition for ‘mwhich’
mroast_score,eSet-CMAPCollection: no visible global function definition
for ‘mroast’
romer_score,eSet-CMAPCollection: no visible global function definition
for ‘romer’
Undefined global functions or variables:
camera mroast mwhich romer
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mgsa_score-methods 20.577 0.214 5.851
romer_score-methods 9.214 0.387 8.810
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [36s/28s]
[36s/29s] OK
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck/00check.log’
for details.
gCMAP.Rcheck/00install.out:
* installing *source* package ‘gCMAP’ ...
** 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
* DONE (gCMAP)
gCMAP.Rcheck/gCMAP-Ex.timings:
name | user | system | elapsed
|
CMAPCollection-class | 0.830 | 0.151 | 0.748 |
|
CMAPResults-class | 2.417 | 0.017 | 2.433 |
|
KEGG2cmap | 0.001 | 0.000 | 0.001 |
|
SignedGeneSet-class | 0.055 | 0.000 | 0.055 |
|
annotate_eset_list | 0.109 | 0.003 | 0.113 |
|
camera_score-methods | 0.301 | 0.040 | 0.665 |
|
center_eSet | 0.02 | 0.00 | 0.02 |
|
connectivity_score-methods | 1.117 | 0.426 | 0.542 |
|
eSetOnDisk | 0.003 | 0.000 | 0.003 |
|
eset_instances | 0.05 | 0.00 | 0.05 |
|
featureScores-methods | 0.277 | 0.135 | 0.411 |
|
fisher_score-methods | 0.805 | 0.280 | 0.485 |
|
gCMAPData-dataset | 0.264 | 0.100 | 0.353 |
|
geneIndex-methods | 0.453 | 0.133 | 0.362 |
|
generate_gCMAP_NChannelSet | 0.112 | 0.012 | 0.124 |
|
gsealm_jg_score-methods | 0.856 | 0.245 | 0.517 |
|
gsealm_score-methods | 1.842 | 0.125 | 1.983 |
|
induceCMAPCollection-methods | 0.502 | 0.136 | 0.395 |
|
mapNmerge | 0.001 | 0.000 | 0.001 |
|
memorize | 0.003 | 0.000 | 0.003 |
|
mergeCMAPs | 0.062 | 0.004 | 0.066 |
|
mgsa_score-methods | 20.577 | 0.214 | 5.851 |
|
minSetSize-methods | 0.703 | 0.256 | 0.530 |
|
mroast_score-methods | 0.952 | 0.171 | 1.088 |
|
romer_score-methods | 9.214 | 0.387 | 8.810 |
|
signedRankSumTest | 0.002 | 0.000 | 0.003 |
|
splitPerturbations | 0.078 | 0.012 | 0.090 |
|
wilcox_score-methods | 0.986 | 0.484 | 0.683 |
|