BioC 3.5: CHECK report for qrqc on toluca2
This page was generated on 2017-04-23 14:35:42 -0400 (Sun, 23 Apr 2017).
qrqc 1.29.0
Vince Buffalo
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qrqc | | Last Changed Rev: 122712 / Revision: 129046 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: qrqc |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qrqc_1.29.0.tar.gz |
| StartedAt: 2017-04-23 08:25:02 -0400 (Sun, 23 Apr 2017) |
| EndedAt: 2017-04-23 08:31:10 -0400 (Sun, 23 Apr 2017) |
| EllapsedTime: 368.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qrqc.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qrqc_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qrqc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.29.0’
* 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 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
kmerKLPlot 8.135 0.194 8.395
basePlot-methods 6.952 0.098 7.157
* 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
‘/Users/biocbuild/bbs-3.5-bioc/meat/qrqc.Rcheck/00check.log’
for details.
qrqc.Rcheck/00install.out:
* 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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.4/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-3.5-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)
qrqc.Rcheck/qrqc-Ex.timings:
| name | user | system | elapsed
|
| FASTASummary-class | 0.002 | 0.000 | 0.003 |
|
| FASTQSummary-class | 0.001 | 0.001 | 0.001 |
|
| SequenceSummary-class | 0.001 | 0.000 | 0.001 |
|
| basePlot-methods | 6.952 | 0.098 | 7.157 |
|
| calcKL | 1.027 | 0.025 | 1.062 |
|
| gcPlot-methods | 1.868 | 0.021 | 1.904 |
|
| getBase-methods | 1.476 | 0.012 | 1.494 |
|
| getBaseProp-methods | 1.252 | 0.058 | 1.326 |
|
| getGC-methods | 0.591 | 0.009 | 0.605 |
|
| getKmer-methods | 1.070 | 0.016 | 1.102 |
|
| getMCQual-methods | 0.724 | 0.036 | 0.771 |
|
| getQual-methods | 1.079 | 0.017 | 1.113 |
|
| getSeqlen-methods | 0.616 | 0.025 | 0.650 |
|
| kmerEntropyPlot | 2.602 | 0.091 | 2.705 |
|
| kmerKLPlot | 8.135 | 0.194 | 8.395 |
|
| list2df | 0.972 | 0.056 | 1.035 |
|
| makeReport | 3.046 | 0.096 | 3.279 |
|
| plotBases | 0.001 | 0.000 | 0.001 |
|
| plotGC | 0.001 | 0.000 | 0.001 |
|
| plotQuals | 0.000 | 0.000 | 0.001 |
|
| plotSeqLengths | 0 | 0 | 0 |
|
| qualPlot-methods | 2.203 | 0.084 | 2.319 |
|
| readSeqFile | 0.329 | 0.014 | 0.348 |
|
| scale_color_dna | 0.599 | 0.017 | 0.618 |
|
| scale_color_iupac | 0.594 | 0.008 | 0.605 |
|
| seqlenPlot-methods | 1.453 | 0.017 | 1.485 |
|