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 3.6: CHECK report for gCMAP on malbec1

This page was generated on 2017-08-16 13:20:26 -0400 (Wed, 16 Aug 2017).

Package 504/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCMAP 1.21.0
Thomas Sandmann
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gCMAP
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gCMAP
Version: 1.21.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.21.0.tar.gz
StartedAt: 2017-08-15 23:20:07 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:23:32 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 204.3 seconds
RetCode: 0
Status:  OK 
CheckDir: gCMAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/gCMAP.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gCMAP’ 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
Namespace in Imports field not imported from: ‘bigmemory’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  18.092  0.168  22.517
romer_score-methods  4.936  0.132   4.882
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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:

nameusersystemelapsed
CMAPCollection-class1.7680.4441.410
CMAPResults-class2.0200.0642.082
KEGG2cmap000
SignedGeneSet-class0.0200.0000.017
annotate_eset_list0.0960.0080.242
camera_score-methods0.7000.1080.824
center_eSet0.0320.0040.034
connectivity_score-methods0.9320.3920.629
eSetOnDisk1.1440.0441.203
eset_instances0.0480.0000.046
featureScores-methods0.2200.0680.478
fisher_score-methods0.8520.3280.447
gCMAPData-dataset0.3120.0680.377
geneIndex-methods0.4600.1280.351
generate_gCMAP_NChannelSet0.7080.0120.723
gsealm_jg_score-methods0.5640.2440.371
gsealm_score-methods1.8440.1241.902
induceCMAPCollection-methods0.2000.0520.197
mapNmerge0.0000.0000.001
memorize0.8080.0320.842
mergeCMAPs0.1760.0000.179
mgsa_score-methods18.092 0.16822.517
minSetSize-methods0.3360.0960.231
mroast_score-methods0.9560.1120.784
romer_score-methods4.9360.1324.882
signedRankSumTest0.0000.0000.001
splitPerturbations0.0480.0040.054
wilcox_score-methods0.7040.5240.681