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BioC 3.0: CHECK report for GenomicAlignments on moscato1

This page was generated on 2015-04-10 09:49:51 -0700 (Fri, 10 Apr 2015).

Package 366/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.2.2
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicAlignments
Last Changed Rev: 100079 / Revision: 102249
Last Changed Date: 2015-03-02 14:03:13 -0800 (Mon, 02 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: GenomicAlignments
Version: 1.2.2
Command: rm -rf GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && mkdir GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.2.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.2.2.tar.gz
StartedAt: 2015-04-10 01:31:32 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:40:54 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 562.1 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomicAlignments.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && mkdir GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.2.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.2.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  '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 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
* 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 ... 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386/GenomicAlignments.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64/GenomicAlignments.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' ... [123s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
junctions-methods          36.76   1.43   46.46
sequenceLayer              15.80   0.45   16.42
summarizeOverlaps-methods  13.93   0.49   15.38
readGAlignments             8.24   0.17    8.40
findSpliceOverlaps-methods  8.05   0.10    9.39
GAlignmentsList-class       4.40   0.01    7.93
** running examples for arch 'x64' ... [107s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
junctions-methods              33.54   1.09   34.71
sequenceLayer                  17.29   0.39   17.68
summarizeOverlaps-methods      12.62   0.23   13.23
findSpliceOverlaps-methods      8.31   0.14    8.46
readGAlignments                 5.52   0.09    5.63
findCompatibleOverlaps-methods  5.30   0.10    5.40
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'GenomicAlignments_unit_tests.R' [38s]
 [39s] OK
** running tests for arch 'x64' ...
  Running 'GenomicAlignments_unit_tests.R' [43s]
 [43s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.

GenomicAlignments.Rcheck/00install.out:


install for i386

* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:671:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:669:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:534:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:580:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:665:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:729:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:882:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:850:7: note: 'OP' was declared here
cigar_utils.c:874:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:849:17: note: 'OPL' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1066:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1034:7: note: 'OP' was declared here
cigar_utils.c:1058:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1033:17: note: 'OPL' was declared here
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1185:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'query_locs_to_ref_locs':
cigar_utils.c:1267:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 [-Wuninitialized]
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
gcc -m32 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o encodeOverlaps_methods.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/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 'GenomicAlignments' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:671:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:669:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:534:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:580:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:665:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:729:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1185:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'query_locs_to_ref_locs':
cigar_utils.c:1267:8: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -m64 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o encodeOverlaps_methods.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.2.2.zip
* DONE (GenomicAlignments)

GenomicAlignments.Rcheck/examples_i386/GenomicAlignments-Ex.timings:

nameusersystemelapsed
GAlignmentPairs-class1.290.001.29
GAlignments-class0.530.000.53
GAlignmentsList-class4.400.017.93
GappedReads-class0.120.000.12
OverlapEncodings-class0.060.001.06
cigar-utils0.270.000.27
coverage-methods0.390.000.39
encodeOverlaps-methods0.010.000.01
findCompatibleOverlaps-methods3.930.033.96
findMateAlignment0.230.000.23
findOverlaps-methods0.830.000.83
findSpliceOverlaps-methods8.050.109.39
intra-range-methods0.20.00.2
junctions-methods36.76 1.4346.46
mapCoords-methods0.250.000.25
pileLettersAt0.870.020.94
readGAlignments8.240.178.40
sequenceLayer15.80 0.4516.42
setops-methods0.090.000.09
stackStringsFromBam1.740.001.73
summarizeOverlaps-methods13.93 0.4915.38

GenomicAlignments.Rcheck/examples_x64/GenomicAlignments-Ex.timings:

nameusersystemelapsed
GAlignmentPairs-class1.690.031.73
GAlignments-class0.970.020.99
GAlignmentsList-class4.740.084.82
GappedReads-class0.170.010.19
OverlapEncodings-class0.100.000.09
cigar-utils0.320.000.33
coverage-methods0.470.000.46
encodeOverlaps-methods0.020.000.02
findCompatibleOverlaps-methods5.30.15.4
findMateAlignment0.290.010.32
findOverlaps-methods1.560.001.56
findSpliceOverlaps-methods8.310.148.46
intra-range-methods0.250.000.25
junctions-methods33.54 1.0934.71
mapCoords-methods0.250.000.25
pileLettersAt0.730.020.75
readGAlignments5.520.095.63
sequenceLayer17.29 0.3917.68
setops-methods0.120.000.12
stackStringsFromBam2.140.022.15
summarizeOverlaps-methods12.62 0.2313.23