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CHECK report for csaw on malbec2

This page was generated on 2019-10-16 12:05:36 -0400 (Wed, 16 Oct 2019).

Package 369/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.18.0
Aaron Lun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/csaw
Branch: RELEASE_3_9
Last Commit: 174c656
Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: csaw
Version: 1.18.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings csaw_1.18.0.tar.gz
StartedAt: 2019-10-16 00:53:16 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:02:04 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 527.9 seconds
RetCode: 0
Status:  OK 
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings csaw_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/csaw.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 ‘csaw’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/csaw/libs/csaw.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
detailRanges 12.173  0.172  12.434
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/csaw.Rcheck/00check.log’
for details.



Installation output

csaw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL csaw
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c annotator.cpp -o annotator.o
annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
annotator.cpp:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (counter < nolaps && query[counter]==curreg) {
                ~~~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’:
best_in_cluster.cpp:11:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=clustids.size() || nwin!=winweight.size()) {
                               ~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c get_cluster_stats.cpp -o get_cluster_stats.o
get_cluster_stats.cpp: In function ‘SEXPREC* get_cluster_stats(SEXP, SEXP, SEXP, SEXP, SEXP)’:
get_cluster_stats.cpp:17:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (nwin!=current.size()) {
       ~~~~^~~~~~~~~~~~~~~~
get_cluster_stats.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (clustid.size()!=nwin) {
         ~~~~~~~~~~~~~~^~~~~~
get_cluster_stats.cpp:33:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (nwin!=winweight.size()) {
      ~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c intersector.cpp -o intersector.o
intersector.cpp: In constructor ‘intersector::intersector(SEXP, SEXP)’:
intersector.cpp:8:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (N!=elements.size()) {
         ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 0 || current >= nelements) {
                            ~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c merge_windows.cpp -o merge_windows.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pair_reads.cpp -o pair_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c single_reads.cpp -o single_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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 intersector.o merge_windows.o pair_reads.o single_reads.o utils.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-csaw/00new/csaw/libs
** R
** 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 (csaw)

Tests output

csaw.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(csaw)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> 
> test_check("csaw")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2724 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
256.563   1.685 260.111 

Example timings

csaw.Rcheck/csaw-Ex.timings

nameusersystemelapsed
SEmethods0.5100.0120.767
calculateCPM0.3530.0000.354
checkBimodality0.4340.0000.591
clusterFDR1.0970.0031.103
clusterWindows2.4800.0522.532
combineTests0.0980.0000.098
consolidateClusters2.2230.0002.223
consolidateTests0.4670.0000.467
consolidateWindows0.4830.0000.484
correlateReads0.1250.0000.125
csawUsersGuide000
detailRanges12.173 0.17212.434
empiricalFDR0.8250.0040.830
extractReads0.7900.0000.791
filterWindows0.4190.0000.420
findMaxima0.0970.0000.098
getBestTest0.0660.0000.066
getPESizes0.0580.0000.059
getWidths0.4220.0000.422
maximizeCcf0.0000.0020.002
mergeWindows0.0450.0010.046
mixedClusters0.0790.0000.079
normOffsets0.1080.0000.108
overlapStats0.6100.0040.615
profileSites0.4740.0080.482
readParam0.0390.0000.040
regionCounts0.3320.0000.331
scaledAverage0.3510.0000.352
strandedCounts1.2010.0041.205
upweightSummit0.0050.0000.004
windowCounts0.8980.0080.905
wwhm0.0840.0000.085