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 3.0: CHECK report for SGSeq on moscato1

This page was generated on 2015-04-10 09:51:31 -0700 (Fri, 10 Apr 2015).

Package 816/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGSeq 1.0.6
Leonard Goldstein
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SGSeq
Last Changed Rev: 96872 / Revision: 102249
Last Changed Date: 2014-11-18 15:30:17 -0800 (Tue, 18 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: SGSeq
Version: 1.0.6
Command: rm -rf SGSeq.buildbin-libdir SGSeq.Rcheck && mkdir SGSeq.buildbin-libdir SGSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.0.6.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.0.6.tar.gz
StartedAt: 2015-04-10 05:33:17 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:41:43 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 506.0 seconds
RetCode: 0
Status:  OK  
CheckDir: SGSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SGSeq.buildbin-libdir SGSeq.Rcheck && mkdir SGSeq.buildbin-libdir SGSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.0.6.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/SGSeq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SGSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SGSeq' version '1.0.6'
* 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 whether package 'SGSeq' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'GenomicRanges:::extraColumnSlotsAsDF'
  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 ... 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 ...
** running examples for arch 'i386' ... [65s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
analyzeFeatures    22.56   0.17   22.75
predictTxFeatures  11.81   0.05   11.86
getSGFeatureCounts  7.02   0.05    7.06
** running examples for arch 'x64' ... [78s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
analyzeFeatures    27.16   0.12   27.28
predictTxFeatures  13.84   0.07   13.91
getSGFeatureCounts  9.06   0.11    9.18
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/SGSeq.Rcheck/00check.log'
for details.

SGSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'SGSeq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SGSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SGSeq' as SGSeq_1.0.6.zip
* DONE (SGSeq)

SGSeq.Rcheck/examples_i386/SGSeq-Ex.timings:

nameusersystemelapsed
SGFeatureCounts0.140.000.14
SGFeatures0.050.000.05
TxFeatures0.050.000.05
TxVariantCounts0.390.000.39
TxVariants0.140.000.14
analyzeFeatures22.56 0.1722.75
analyzeVariants2.310.002.31
annotate1.580.001.58
assays000
convertToSGFeatures2.000.022.01
convertToTxFeatures0.710.010.73
exportFeatures000
filterTerminalExons0.260.000.26
findTxVariants2.170.002.17
getBamInfo0.240.000.24
getSGFeatureCounts7.020.057.06
getTxVariantCounts0.040.000.05
mergeTxFeatures0.380.000.37
plotFeatures000
plotSpliceGraph000
plotVariants000
predictTxFeatures11.81 0.0511.86
slots0.010.000.02

SGSeq.Rcheck/examples_x64/SGSeq-Ex.timings:

nameusersystemelapsed
SGFeatureCounts0.260.000.27
SGFeatures0.100.000.09
TxFeatures0.090.000.10
TxVariantCounts0.750.040.78
TxVariants0.260.000.26
analyzeFeatures27.16 0.1227.28
analyzeVariants2.120.002.12
annotate1.940.001.94
assays000
convertToSGFeatures3.110.003.11
convertToTxFeatures0.670.020.68
exportFeatures000
filterTerminalExons0.310.000.31
findTxVariants2.550.002.55
getBamInfo0.240.000.23
getSGFeatureCounts9.060.119.18
getTxVariantCounts0.060.000.06
mergeTxFeatures0.440.000.44
plotFeatures000
plotSpliceGraph000
plotVariants000
predictTxFeatures13.84 0.0713.91
slots000