| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:36:59 -0400 (Tue, 09 Apr 2019).
| Package 645/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicAlignments 1.19.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: GenomicAlignments |
| Version: 1.19.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GenomicAlignments_1.19.1.tar.gz |
| StartedAt: 2019-04-09 00:45:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:50:29 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 298.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicAlignments.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GenomicAlignments_1.19.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicAlignments.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.1’
* 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 ... WARNING
Undocumented S4 methods:
generic 'updateObject' and siglist 'GAlignments'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'intra-range-methods':
‘\S4method{narrow}{GAlignmentsList}’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
junctions-methods 18.353 0.311 19.491
readGAlignments 13.394 0.452 14.026
summarizeOverlaps-methods 10.214 0.492 10.520
coordinate-mapping-methods 8.180 0.103 8.335
findSpliceOverlaps-methods 7.182 0.059 7.272
sequenceLayer 6.728 0.486 7.531
* 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: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.
GenomicAlignments.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GenomicAlignments
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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:626:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*flag_elt == NA_INTEGER) {
^˜˜˜˜˜˜˜˜
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:708:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*flag_elt == NA_INTEGER) {
^˜˜˜˜˜˜˜˜
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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I/usr/local/include -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicAlignments)
GenomicAlignments.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, 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
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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 -- Tue Apr 9 00:50:22 2019
***********************************************
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
29.504 1.129 31.202
GenomicAlignments.Rcheck/GenomicAlignments-Ex.timings
| name | user | system | elapsed | |
| GAlignmentPairs-class | 0.662 | 0.048 | 0.711 | |
| GAlignments-class | 0.284 | 0.004 | 0.288 | |
| GAlignmentsList-class | 3.403 | 0.072 | 3.723 | |
| GappedReads-class | 0.130 | 0.004 | 0.134 | |
| OverlapEncodings-class | 1.492 | 0.000 | 1.492 | |
| cigar-utils | 0.224 | 0.004 | 0.227 | |
| coordinate-mapping-methods | 8.180 | 0.103 | 8.335 | |
| coverage-methods | 2.867 | 0.076 | 2.953 | |
| encodeOverlaps-methods | 0.037 | 0.003 | 0.040 | |
| findCompatibleOverlaps-methods | 1.802 | 0.012 | 1.813 | |
| findMateAlignment | 0.139 | 0.000 | 0.140 | |
| findOverlaps-methods | 0.523 | 0.000 | 0.523 | |
| findSpliceOverlaps-methods | 7.182 | 0.059 | 7.272 | |
| intra-range-methods | 0.405 | 0.008 | 0.426 | |
| junctions-methods | 18.353 | 0.311 | 19.491 | |
| pileLettersAt | 0.711 | 0.012 | 0.723 | |
| readGAlignments | 13.394 | 0.452 | 14.026 | |
| sequenceLayer | 6.728 | 0.486 | 7.531 | |
| setops-methods | 0.066 | 0.000 | 0.066 | |
| stackStringsFromBam | 1.268 | 0.008 | 1.276 | |
| summarizeOverlaps-methods | 10.214 | 0.492 | 10.520 | |