Package: CSAR

Version: 1.38.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CSAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CSAR_1.38.0.tar.gz

StartedAt: 2020-04-15 00:44:27 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:47:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 157.3 seconds

RetCode: 0

Status:  OK

CheckDir: CSAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CSAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CSAR_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CSAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSAR’ version ‘1.38.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CSAR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mappedReads2Nhits: no visible global function definition for
  ‘chromosome’
mappedReads2Nhits: no visible global function definition for ‘position’
Undefined global functions or variables:
  chromosome position
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getThreshold           15.132  0.016  15.178
CSAR-package           14.928  0.012  14.958
getPermutatedWinScores 13.740  0.028  13.811
permutatedWinScores    13.540  0.024  13.604
genesWithPeaks          5.256  0.000   5.272
* 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-3.10-bioc/meat/CSAR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CSAR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘CSAR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c CSAR.c -o CSAR.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o CSAR.so CSAR.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-CSAR/00new/CSAR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CSAR)

name	user	system	elapsed
CSAR-package	14.928	0.012	14.958
ChIPseqScore	3.896	0.000	3.899
distance2Genes	4.940	0.000	4.944
genesWithPeaks	5.256	0.000	5.272
getPermutatedWinScores	13.740	0.028	13.811
getThreshold	15.132	0.016	15.178
loadMappedReads	0	0	0
mappedReads2Nhits	1.480	0.004	1.486
permutatedWinScores	13.540	0.024	13.604
sampleSEP3_test	0.004	0.000	0.001
score2wig	3.636	0.008	3.649
sigWin	4.624	0.008	4.637