GenomicAlignments 1.6.3
Bioconductor Package Maintainer
| 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/GenomicAlignments | | Last Changed Rev: 112191 / Revision: 116712 | | Last Changed Date: 2016-01-05 12:51:48 -0800 (Tue, 05 Jan 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.6.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GenomicAlignments.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.6.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
‘SummarizedExperiment’ ‘Biostrings’ ‘Rsamtools’
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 ‘GenomicAlignments’ can be installed ... [12s/12s] 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:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’
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 dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘Biostrings:::.normarg_padding.letter’
‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’
‘Rsamtools:::.isValidHit’
‘Rsamtools:::.load_bamcols_from_scanBam_res’
See the note in ?`:::` about the use of this operator.
* 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 ... 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 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 ... [74s/73s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
junctions-methods 22.336 0.132 22.653
readGAlignments 9.666 0.092 9.752
summarizeOverlaps-methods 8.374 0.450 7.884
coordinate-mapping-methods 6.995 0.080 7.079
sequenceLayer 6.525 0.136 6.674
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicAlignments_unit_tests.R’ [29s/28s]
[29s/28s] 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.
* installing *source* package ‘GenomicAlignments’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:676:9: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
f_elt++;
^
cigar_utils.c:658:27: warning: ‘range_buf2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
range_buf1 = range_buf2->elts[*f_elt - 1];
^
cigar_utils.c:674:40: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:674:20: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:670:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:734:12: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
flag_elt++;
^
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:880:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Roffset)
^
cigar_utils.c:852:15: note: ‘Roffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c:878:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Loffset)
^
cigar_utils.c:852:6: note: ‘Loffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1064:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Roffset)
^
cigar_utils.c:1036:15: note: ‘Roffset’ was declared here
int Loffset, Roffset, buf_offset;
^
cigar_utils.c:1062:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (offset == Loffset)
^
cigar_utils.c:1036:6: note: ‘Loffset’ was declared here
int Loffset, Roffset, buf_offset;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:180:17: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
^
encodeOverlaps_methods.c:99:6: note: ‘out_nelt0’ was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/GenomicAlignments.Rcheck/GenomicAlignments/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 (GenomicAlignments)