qrqc 1.30.0
Vince Buffalo
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/qrqc | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings qrqc_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/qrqc.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.30.0’
* 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 ... 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
binned2boxplot: no visible global function definition for 'quantile'
calcKL : kmerDist: no visible global function definition for
'aggregate'
generateReads: no visible global function definition for 'DNAStringSet'
generateReads: no visible global function definition for
'write.XStringSet'
makeReportDir: no visible global function definition for 'na.exclude'
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 global function definition for
'aggregate'
getBase,SequenceSummary: no visible binding for global variable 'base'
getBaseProp,SequenceSummary: no visible global function definition for
'aggregate'
getBaseProp,SequenceSummary: no visible binding for global variable
'base'
getGC,SequenceSummary : <local>: no visible global function definition
for 'aggregate'
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'
plotGC,SequenceSummary : <local>: no visible global function definition
for 'aggregate'
qualPlot,FASTQSummary: no visible binding for global variable
'position'
qualPlot,list: no visible binding for global variable 'position'
Undefined global functions or variables:
DNAStringSet aggregate base entropy kl kmer na.exclude position
quantile write.XStringSet
Consider adding
importFrom("stats", "aggregate", "na.exclude", "quantile")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
kmerKLPlot 6.2 0.056 6.257
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-functions.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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/qrqc.Rcheck/00check.log’
for details.
* installing *source* package ‘qrqc’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_io.c -o R_init_io.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/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 [-Wincompatible-pointer-types]
#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:350:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
block = kseq_init(fp);
^
In file included from io.c:11:0:
/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.5-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-3.5-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:452:21: warning: passing argument 1 of ‘kseq_init’ from incompatible pointer type [-Wincompatible-pointer-types]
block = kseq_init(fp);
^
In file included from io.c:11:0:
/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
SCOPE kseq_t *kseq_init(type_t fd) \
^
/home/biocbuild/bbs-3.5-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-3.5-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:453:14: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
FILE_CLOSE(fp);
^
io.c:33:32: note: in definition of macro ‘FILE_CLOSE’
#define FILE_CLOSE(x) (gzclose(x))
^
In file included from io.c:30:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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-3.5-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-3.5-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-3.5-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 -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/qrqc.Rcheck/qrqc/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 (qrqc)