BioC 3.5: CHECK report for GenomicRanges on tokay2
This page was generated on 2017-10-10 14:20:46 -0400 (Tue, 10 Oct 2017).
GenomicRanges 1.28.6
Bioconductor Package Maintainer
| Snapshot Date: 2017-10-09 17:17:10 -0400 (Mon, 09 Oct 2017) | | URL: https://git.bioconductor.org/packages/GenomicRanges | | Branch: RELEASE_3_5 | | Last Commit: 197472d | | Last Changed Date: 2017-10-03 14:39:56 -0400 (Tue, 03 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | ERROR | OK | WARNINGS | OK | |
Summary
| Package: GenomicRanges
|
| Version: 1.28.6
|
| Command: rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.28.6.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.28.6.tar.gz
|
| StartedAt: 2017-10-10 02:18:15 -0400 (Tue, 10 Oct 2017)
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| EndedAt: 2017-10-10 02:28:11 -0400 (Tue, 10 Oct 2017)
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| EllapsedTime: 595.3 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: GenomicRanges.Rcheck
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| Warnings: 1
|
Command output
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###
### Running command:
###
### rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.28.6.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.28.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.28.6'
* package encoding: UTF-8
* 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 whether package 'GenomicRanges' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{reduce}{GenomicRangesList}
Code: function(x, drop.empty.ranges = FALSE, ...)
Docs: function(x, drop.empty.ranges = FALSE, min.gapwidth = 1L,
with.inframe.attrib = FALSE, ignore.strand = FALSE)
Argument names in code not in docs:
...
Argument names in docs not in code:
min.gapwidth with.inframe.attrib ignore.strand
Mismatches in argument names:
Position: 3 Code: ... Docs: min.gapwidth
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386/GenomicRanges.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicvars 51.61 16.14 72.46
GPos-class 46.99 8.91 58.00
makeGRangesFromDataFrame 2.67 0.43 23.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicvars 49.17 14.89 64.21
GPos-class 46.06 9.96 56.02
makeGRangesFromDataFrame 2.99 0.33 30.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.
GenomicRanges.Rcheck/00install.out:
install for i386
* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.28.6.zip
* DONE (GenomicRanges)
GenomicRanges.Rcheck/examples_i386/GenomicRanges-Ex.timings:
| name | user | system | elapsed
|
| GNCList-class | 0.89 | 0.02 | 0.91 |
|
| GPos-class | 46.99 | 8.91 | 58.00 |
|
| GRanges-class | 1.43 | 0.14 | 1.57 |
|
| GRangesList-class | 0.45 | 0.00 | 0.45 |
|
| GenomicRanges-comparison | 0.23 | 0.00 | 0.23 |
|
| absoluteRanges | 1.61 | 0.12 | 1.74 |
|
| constraint | 0.99 | 0.05 | 1.03 |
|
| coverage-methods | 0.18 | 0.00 | 0.19 |
|
| findOverlaps-methods | 1.11 | 0.00 | 1.11 |
|
| genomicvars | 51.61 | 16.14 | 72.46 |
|
| inter-range-methods | 2.08 | 0.37 | 2.45 |
|
| intra-range-methods | 0.38 | 0.00 | 0.38 |
|
| makeGRangesFromDataFrame | 2.67 | 0.43 | 23.06 |
|
| makeGRangesListFromDataFrame | 0.12 | 0.00 | 0.12 |
|
| nearest-methods | 0.72 | 0.00 | 0.72 |
|
| phicoef | 0.02 | 0.00 | 0.01 |
|
| range-squeezers | 0 | 0 | 0 |
|
| setops-methods | 2.02 | 0.00 | 2.02 |
|
| strand-utils | 0.09 | 0.00 | 0.09 |
|
| tile-methods | 0.08 | 0.00 | 0.08 |
|
| tileGenome | 0.25 | 0.01 | 0.27 |
|
GenomicRanges.Rcheck/examples_x64/GenomicRanges-Ex.timings:
| name | user | system | elapsed
|
| GNCList-class | 1.19 | 0.01 | 1.20 |
|
| GPos-class | 46.06 | 9.96 | 56.02 |
|
| GRanges-class | 2.08 | 0.14 | 2.22 |
|
| GRangesList-class | 0.58 | 0.00 | 0.58 |
|
| GenomicRanges-comparison | 0.26 | 0.00 | 0.27 |
|
| absoluteRanges | 1.28 | 0.08 | 1.35 |
|
| constraint | 1.17 | 0.03 | 1.21 |
|
| coverage-methods | 0.22 | 0.00 | 0.22 |
|
| findOverlaps-methods | 1.19 | 0.00 | 1.18 |
|
| genomicvars | 49.17 | 14.89 | 64.21 |
|
| inter-range-methods | 1.97 | 0.18 | 2.15 |
|
| intra-range-methods | 0.5 | 0.0 | 0.5 |
|
| makeGRangesFromDataFrame | 2.99 | 0.33 | 30.93 |
|
| makeGRangesListFromDataFrame | 0.18 | 0.00 | 0.18 |
|
| nearest-methods | 0.85 | 0.00 | 0.85 |
|
| phicoef | 0.03 | 0.00 | 0.03 |
|
| range-squeezers | 0 | 0 | 0 |
|
| setops-methods | 2.09 | 0.00 | 2.09 |
|
| strand-utils | 0.11 | 0.00 | 0.11 |
|
| tile-methods | 0.08 | 0.00 | 0.08 |
|
| tileGenome | 0.17 | 0.02 | 0.19 |
|