qrqc 1.24.0
Vince Buffalo
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/qrqc | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qrqc_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/qrqc.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.24.0’
* 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 ... [29s/31s] 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 ... [43s/47s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
kmerKLPlot 7.62 0.289 10.528
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-functions.R’ [14s/14s]
[14s/15s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/qrqc.Rcheck/00check.log’
for details.
* installing *source* package ‘qrqc’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_io.c -o R_init_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c io.c -o io.o
io.c:34:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_BASIC(SCOPE, type_t) \
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/kseq.h:158:13: note: expanded from macro '__KSEQ_BASIC'
SCOPE void kseq_destroy(kseq_t *ks) \
^
io.c:37:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, double)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:49:1: note: expanded from here
kh_clear_str
^
io.c:37:1: warning: unused function 'kh_del_str' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:63:1: note: expanded from here
kh_del_str
^
3 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qrqc.so R_init_io.o io.o /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.2-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)