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BioC 3.5: CHECK report for TFBSTools on malbec2

This page was generated on 2017-08-16 13:15:22 -0400 (Wed, 16 Aug 2017).

Package 1314/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.14.2
Ge Tan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/TFBSTools
Last Changed Rev: 131810 / Revision: 131943
Last Changed Date: 2017-08-08 09:09:27 -0400 (Tue, 08 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFBSTools
Version: 1.14.2
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TFBSTools_1.14.2.tar.gz
StartedAt: 2017-08-16 02:38:46 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:43:54 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 308.0 seconds
RetCode: 0
Status:  OK 
CheckDir: TFBSTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TFBSTools_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TFBSTools.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 ‘TFBSTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFBSTools’ version ‘1.14.2’
* 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 ‘TFBSTools’ 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
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’
  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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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
SiteSetList-class     52.288  0.004  52.321
searchAln-methods      7.168  0.004   7.184
SiteSet-class          6.004  0.052   6.062
toGRangesList-methods  5.444  0.020   5.469
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.


TFBSTools.Rcheck/00install.out:

* installing *source* package ‘TFBSTools’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function ‘score’:
matrixAlignerDynamic.c:235:22: warning: ‘best_pntr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
                      ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_TFBSTools.c -o R_init_TFBSTools.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/TFBSTools.Rcheck/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TFBSTools)

TFBSTools.Rcheck/TFBSTools-Ex.timings:

nameusersystemelapsed
IUPAC2Matrix0.0040.0000.001
MA0004.10.0040.0000.005
MotifSet-class0.0040.0000.000
PFMSimilarity-methods0.8760.0080.994
PWMSimilarity-methods0.0200.0000.018
SiteSet-class6.0040.0526.062
SiteSetList-class52.288 0.00452.321
TFFM-class0.0280.0000.028
XMatrix-class0.0080.0000.009
XMatrixList-class0.0000.0040.003
deleteMatrixHavingID-methods0.0600.0000.059
dmmEM-methods000
getEmissionProb0.3000.0000.298
getMatrixByID-methods0.1920.0080.310
getMatrixSet-methods000
getPosProb0.2200.0040.224
makeFlatFileDir000
parseMEMEOutput0.1040.0000.103
permuteMatrix-methods0.0200.0000.021
rPWMDmm-methods000
readJASPARMatrix0.0120.0080.021
readXMLTFFM0.0240.0000.024
runMEME-methods000
sampleRanges0.3440.0040.345
searchAln-methods7.1680.0047.184
searchPairBSgenome-methods000
searchSeq-methods0.5680.0040.574
seqLogo1.5720.0041.577
shannon.entropy0.0000.0000.001
toGRangesList-methods5.4440.0205.469
toICM-methods0.0360.0000.038
toPWM-methods0.0080.0000.007