| Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:11:44 -0400 (Thu, 12 Apr 2018).
| Package 562/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicAlignments 1.14.2 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GenomicAlignments |
| Version: 1.14.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz |
| StartedAt: 2018-04-11 23:48:22 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:52:30 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 248.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicAlignments.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.14.2’
* package encoding: UTF-8
* 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 ... 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:::.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
junctions-methods 16.208 0.220 17.317
readGAlignments 9.732 0.376 10.130
summarizeOverlaps-methods 7.168 0.152 7.742
coordinate-mapping-methods 7.132 0.092 7.574
sequenceLayer 6.564 0.304 6.919
findSpliceOverlaps-methods 4.904 0.084 5.026
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.
GenomicAlignments.Rcheck/00install.out
* installing *source* package ‘GenomicAlignments’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/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:674:22: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^
cigar_utils.c:674:16: 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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:182:2: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
CharAE_delete_at(out, out_nelt0, j1 * nrow);
^
encodeOverlaps_methods.c:99:6: note: ‘out_nelt0’ was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)
GenomicAlignments.Rcheck/tests/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GenomicAlignments") || stop("unable to load GenomicRanges package")
Loading required package: GenomicAlignments
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
[1] TRUE
> GenomicAlignments:::.test()
RUNIT TEST PROTOCOL -- Wed Apr 11 23:52:25 2018
***********************************************
Number of test functions: 41
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicAlignments RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41
Number of errors: 0
Number of failures: 0
Warning message:
In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, :
4 alignments with ambiguous pairing were dumped.
Use 'getDumpedAlignments()' to retrieve them from the dump environment.
>
> proc.time()
user system elapsed
33.844 0.532 34.734
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
| name | user | system | elapsed | |
| GAlignmentPairs-class | 1.860 | 0.024 | 1.896 | |
| GAlignments-class | 0.620 | 0.000 | 0.619 | |
| GAlignmentsList-class | 3.436 | 0.032 | 3.540 | |
| GappedReads-class | 0.116 | 0.000 | 0.115 | |
| OverlapEncodings-class | 1.280 | 0.000 | 1.278 | |
| cigar-utils | 0.384 | 0.008 | 0.705 | |
| coordinate-mapping-methods | 7.132 | 0.092 | 7.574 | |
| coverage-methods | 2.216 | 0.020 | 2.237 | |
| encodeOverlaps-methods | 0.028 | 0.000 | 0.026 | |
| findCompatibleOverlaps-methods | 1.048 | 0.016 | 1.067 | |
| findMateAlignment | 0.176 | 0.000 | 0.178 | |
| findOverlaps-methods | 0.364 | 0.000 | 0.367 | |
| findSpliceOverlaps-methods | 4.904 | 0.084 | 5.026 | |
| intra-range-methods | 0.204 | 0.012 | 0.217 | |
| junctions-methods | 16.208 | 0.220 | 17.317 | |
| pileLettersAt | 0.628 | 0.004 | 0.631 | |
| readGAlignments | 9.732 | 0.376 | 10.130 | |
| sequenceLayer | 6.564 | 0.304 | 6.919 | |
| setops-methods | 0.064 | 0.004 | 0.069 | |
| stackStringsFromBam | 1.048 | 0.004 | 1.055 | |
| summarizeOverlaps-methods | 7.168 | 0.152 | 7.742 | |