csaw 1.7.3
Aaron Lun
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/csaw | | Last Changed Rev: 120207 / Revision: 121152 | | Last Changed Date: 2016-08-17 03:17:05 -0700 (Wed, 17 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings csaw_1.7.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/csaw.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.7.3’
* 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 ‘csaw’ 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... 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
detailRanges 6.804 0.092 6.904
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
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: OK
* installing *source* package ‘csaw’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c annotator.cpp -o annotator.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c bam_utils.cpp -o bam_utils.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c best_in_cluster.cpp -o best_in_cluster.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c find_maxima.cpp -o find_maxima.o
find_maxima.cpp: In function ‘SEXPREC* find_maxima(SEXP, SEXP, SEXP, SEXP, SEXP)’:
find_maxima.cpp:90:22: warning: ‘is_max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
while (right_copy >= is_max) {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c get_cluster_stats.cpp -o get_cluster_stats.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c get_profile.cpp -o get_profile.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c merge_windows.cpp -o merge_windows.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c pair_reads.cpp -o pair_reads.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c single_reads.cpp -o single_reads.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o -L/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/csaw.Rcheck/csaw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (csaw)