BioC 3.1: CHECK report for qrqc on zin2

Package: qrqc

Version: 1.22.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.22.0.tar.gz

StartedAt: 2015-10-09 04:35:28 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:38:58 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 210.2 seconds

RetCode: 0

Status:  OK

CheckDir: qrqc.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/qrqc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’
  ‘Rsamtools’ ‘testthat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘qrqc’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rsamtools’ ‘brew’ ‘testthat’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generateReads: no visible global function definition for ‘DNAStringSet’
generateReads: no visible global function definition for
  ‘write.XStringSet’
basePlot,SequenceSummary: no visible binding for global variable ‘base’
basePlot,list: no visible binding for global variable ‘base’
gcPlot,SequenceSummary: no visible binding for global variable
  ‘position’
gcPlot,list: no visible binding for global variable ‘position’
getBase,SequenceSummary: no visible binding for global variable ‘base’
getBaseProp,SequenceSummary: no visible binding for global variable
  ‘base’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘position’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
  ‘entropy’
kmerEntropyPlot,list: no visible binding for global variable ‘position’
kmerEntropyPlot,list: no visible binding for global variable ‘entropy’
kmerKLPlot,SequenceSummary: no visible binding for global variable
  ‘kmer’
kmerKLPlot,SequenceSummary: no visible binding for global variable
  ‘position’
kmerKLPlot,SequenceSummary: no visible binding for global variable ‘kl’
kmerKLPlot,list : <anonymous>: no visible binding for global variable
  ‘kmer’
kmerKLPlot,list: no visible binding for global variable ‘position’
kmerKLPlot,list: no visible binding for global variable ‘kl’
kmerKLPlot,list: no visible binding for global variable ‘kmer’
qualPlot,FASTQSummary: no visible binding for global variable
  ‘position’
qualPlot,list: no visible binding for global variable ‘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 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 ... [32s/32s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kmerKLPlot 6.33   0.04   6.365
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-functions.R’ [8s/8s]
 [9s/9s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/qrqc.Rcheck/00check.log’
for details.

* installing *source* package ‘qrqc’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_io.c -o R_init_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘summarize_file’:
io.c:32:25: warning: initialization from incompatible pointer type [enabled by default]
 #define FILE_OPEN(x, m) (gzopen(x, m))
                         ^
io.c:347:19: note: in expansion of macro ‘FILE_OPEN’
   FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
                   ^
io.c:350:3: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [enabled by default]
   block = kseq_init(fp);
   ^
In file included from io.c:11:0:
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’
 KSEQ_INIT(gzFile, gzread)
 ^
io.c:452:3: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [enabled by default]
   block = kseq_init(fp);
   ^
In file included from io.c:11:0:
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
  SCOPE kseq_t *kseq_init(type_t fd)         \
                ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’
 KSEQ_INIT(gzFile, gzread)
 ^
io.c:453:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
   FILE_CLOSE(fp);
   ^
In file included from io.c:30:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
In file included from io.c:11:0:
io.c: At top level:
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:158:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
  SCOPE void kseq_destroy(kseq_t *ks)         \
             ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro ‘__KSEQ_BASIC’
  __KSEQ_BASIC(SCOPE, type_t)     \
  ^
/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro ‘KSEQ_INIT2’
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
io.c:34:1: note: in expansion of macro ‘KSEQ_INIT’
 KSEQ_INIT(gzFile, gzread)
 ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/qrqc.Rcheck/qrqc/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (qrqc)

name	user	system	elapsed
FASTASummary-class	0.002	0.000	0.002
FASTQSummary-class	0.001	0.000	0.001
SequenceSummary-class	0.001	0.000	0.001
basePlot-methods	2.045	0.060	2.116
calcKL	0.631	0.024	0.655
gcPlot-methods	0.884	0.024	0.910
getBase-methods	0.564	0.016	0.580
getBaseProp-methods	0.582	0.012	0.595
getGC-methods	0.389	0.012	0.402
getKmer-methods	0.856	0.012	0.887
getMCQual-methods	2.279	0.028	2.323
getQual-methods	0.532	0.016	0.549
getSeqlen-methods	0.377	0.012	0.389
kmerEntropyPlot	1.923	0.024	1.947
kmerKLPlot	6.330	0.040	6.365
list2df	0.81	0.04	0.85
makeReport	1.201	0.012	1.211
plotBases	0.001	0.000	0.001
plotGC	0	0	0
plotQuals	0.001	0.000	0.001
plotSeqLengths	0.000	0.000	0.001
qualPlot-methods	1.549	0.008	1.566
readSeqFile	0.248	0.004	0.251
scale_color_dna	0.371	0.008	0.379
scale_color_iupac	0.415	0.004	0.419
seqlenPlot-methods	0.826	0.012	0.837