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BioC 3.4: CHECK report for GenomicAlignments on zin1

This page was generated on 2016-09-21 03:38:42 -0700 (Wed, 21 Sep 2016).

Package 493/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.9.6
Bioconductor Package Maintainer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicAlignments
Last Changed Rev: 119397 / Revision: 121152
Last Changed Date: 2016-07-15 23:33:55 -0700 (Fri, 15 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicAlignments
Version: 1.9.6
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.9.6.tar.gz
StartedAt: 2016-09-20 07:03:21 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:07:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 223.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicAlignments.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicAlignments_1.9.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicAlignments.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.9.6’
* 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:::.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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
junctions-methods          17.688  0.268  18.042
readGAlignments             9.372  0.296   9.668
findSpliceOverlaps-methods  9.452  0.184   9.645
sequenceLayer               5.980  0.396   6.377
summarizeOverlaps-methods   5.860  0.156   7.811
coordinate-mapping-methods  5.624  0.016   5.672
* 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-3.4-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.


GenomicAlignments.Rcheck/00install.out:

* installing *source* package ‘GenomicAlignments’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-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:674:22: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include"   -fpic  -g -O2  -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-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:99:6: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^
gcc -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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/GenomicAlignments-Ex.timings:

nameusersystemelapsed
GAlignmentPairs-class0.5360.0000.538
GAlignments-class0.2800.0000.277
GAlignmentsList-class2.8320.0242.903
GappedReads-class0.0760.0120.089
OverlapEncodings-class0.0480.0000.049
cigar-utils0.1800.0080.189
coordinate-mapping-methods5.6240.0165.672
coverage-methods2.1440.0482.192
encodeOverlaps-methods0.0160.0000.016
findCompatibleOverlaps-methods0.7680.0240.856
findMateAlignment0.0960.0040.104
findOverlaps-methods0.3240.0000.324
findSpliceOverlaps-methods9.4520.1849.645
intra-range-methods0.2560.0040.259
junctions-methods17.688 0.26818.042
pileLettersAt0.4960.0120.515
readGAlignments9.3720.2969.668
sequenceLayer5.9800.3966.377
setops-methods0.0720.0040.078
stackStringsFromBam1.1200.0041.133
summarizeOverlaps-methods5.8600.1567.811