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BioC 3.5: CHECK report for TFBSTools on toluca2

This page was generated on 2017-04-23 14:37:53 -0400 (Sun, 23 Apr 2017).

Package 1310/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.13.2
Ge Tan
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TFBSTools
Last Changed Rev: 124430 / Revision: 129046
Last Changed Date: 2016-11-24 06:04:17 -0500 (Thu, 24 Nov 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
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: 1.13.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.13.2.tar.gz
StartedAt: 2017-04-23 10:44:51 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 10:51:49 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 417.8 seconds
RetCode: 0
Status:  OK 
CheckDir: TFBSTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.13.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TFBSTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.2’
* 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     54.025  2.224  61.346
searchAln-methods     10.427  0.034  10.555
SiteSet-class          8.385  0.338   9.532
toGRangesList-methods  8.220  0.025   8.290
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.


TFBSTools.Rcheck/00install.out:

* installing *source* package ‘TFBSTools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_TFBSTools.c -o R_init_TFBSTools.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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
IUPAC2Matrix0.0010.0000.001
MA0004.10.0050.0020.007
MotifSet-class0.0010.0010.001
PFMSimilarity-methods0.4700.0140.513
PWMSimilarity-methods0.0310.0020.033
SiteSet-class8.3850.3389.532
SiteSetList-class54.025 2.22461.346
TFFM-class0.0430.0010.044
XMatrix-class0.0140.0010.015
XMatrixList-class0.0050.0010.006
deleteMatrixHavingID-methods0.0890.0280.121
dmmEM-methods0.0010.0000.001
getEmissionProb0.5040.0070.512
getMatrixByID-methods0.3450.0170.371
getMatrixSet-methods000
getPosProb0.3770.0140.392
makeFlatFileDir0.0000.0000.001
parseMEMEOutput0.1910.0010.194
permuteMatrix-methods0.0340.0010.037
rPWMDmm-methods0.0000.0000.001
readJASPARMatrix0.0310.0010.032
readXMLTFFM0.0400.0010.041
runMEME-methods0.0010.0000.001
sampleRanges0.5260.0070.533
searchAln-methods10.427 0.03410.555
searchPairBSgenome-methods0.0010.0010.001
searchSeq-methods0.7440.0070.754
seqLogo1.7280.2882.033
shannon.entropy0.0000.0000.001
toGRangesList-methods8.2200.0258.290
toICM-methods0.0660.0020.069
toPWM-methods0.0110.0010.013