BioC 3.5: CHECK report for TFBSTools on malbec2

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

* 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)

name	user	system	elapsed
IUPAC2Matrix	0.004	0.000	0.001
MA0004.1	0.004	0.000	0.005
MotifSet-class	0.004	0.000	0.000
PFMSimilarity-methods	0.876	0.008	0.994
PWMSimilarity-methods	0.020	0.000	0.018
SiteSet-class	6.004	0.052	6.062
SiteSetList-class	52.288	0.004	52.321
TFFM-class	0.028	0.000	0.028
XMatrix-class	0.008	0.000	0.009
XMatrixList-class	0.000	0.004	0.003
deleteMatrixHavingID-methods	0.060	0.000	0.059
dmmEM-methods	0	0	0
getEmissionProb	0.300	0.000	0.298
getMatrixByID-methods	0.192	0.008	0.310
getMatrixSet-methods	0	0	0
getPosProb	0.220	0.004	0.224
makeFlatFileDir	0	0	0
parseMEMEOutput	0.104	0.000	0.103
permuteMatrix-methods	0.020	0.000	0.021
rPWMDmm-methods	0	0	0
readJASPARMatrix	0.012	0.008	0.021
readXMLTFFM	0.024	0.000	0.024
runMEME-methods	0	0	0
sampleRanges	0.344	0.004	0.345
searchAln-methods	7.168	0.004	7.184
searchPairBSgenome-methods	0	0	0
searchSeq-methods	0.568	0.004	0.574
seqLogo	1.572	0.004	1.577
shannon.entropy	0.000	0.000	0.001
toGRangesList-methods	5.444	0.020	5.469
toICM-methods	0.036	0.000	0.038
toPWM-methods	0.008	0.000	0.007

BioC 3.5: CHECK report for TFBSTools on malbec2

Summary

Command output