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BioC 3.1: CHECK report for GenomicAlignments on moscato2

This page was generated on 2015-10-09 09:30:50 -0700 (Fri, 09 Oct 2015).

Package 396/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.4.2
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicAlignments
Last Changed Rev: 109036 / Revision: 109384
Last Changed Date: 2015-09-30 17:42:34 -0700 (Wed, 30 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.4.2
Command: rm -rf GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && mkdir GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.4.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.4.2.tar.gz
StartedAt: 2015-10-09 02:08:30 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:16:38 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 487.9 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.4.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GenomicAlignments.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.4.2'
* 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 'E:/biocbld/bbs-3.1-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386/GenomicAlignments.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-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' ... [131s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
junctions-methods              32.45   0.99   37.50
sequenceLayer                  13.56   0.50   14.10
summarizeOverlaps-methods       9.26   0.27   19.77
coordinate-mapping-methods      7.98   0.20    9.87
findSpliceOverlaps-methods      6.48   0.14   23.51
readGAlignments                 5.96   0.07    6.02
findCompatibleOverlaps-methods  1.36   0.08    5.09
** running examples for arch 'x64' ... [109s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
junctions-methods          31.01   1.34   32.37
sequenceLayer              13.91   0.59   14.51
coordinate-mapping-methods  9.45   0.25    9.71
summarizeOverlaps-methods   8.22   0.08   20.45
findSpliceOverlaps-methods  6.03   0.11    6.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'GenomicAlignments_unit_tests.R' [30s]
 [31s] OK
** running tests for arch 'x64' ...
  Running 'GenomicAlignments_unit_tests.R' [38s]
 [38s] 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.


GenomicAlignments.Rcheck/00install.out:


install for i386

* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/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:678:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:676:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:541:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:672:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:736:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:889:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:857:7: note: 'OP' was declared here
cigar_utils.c:881:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:856:17: note: 'OPL' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1073:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1041:7: note: 'OP' was declared here
cigar_utils.c:1065:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1040:17: note: 'OPL' was declared here
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/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 coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/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:678:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:676:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:541:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:672:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:736:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/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 coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.4.2.zip
* DONE (GenomicAlignments)

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

nameusersystemelapsed
GAlignmentPairs-class0.890.020.97
GAlignments-class0.460.000.46
GAlignmentsList-class3.530.013.62
GappedReads-class0.110.000.11
OverlapEncodings-class0.060.000.06
cigar-utils0.360.020.38
coordinate-mapping-methods7.980.209.87
coverage-methods0.560.000.56
encodeOverlaps-methods0.020.000.02
findCompatibleOverlaps-methods1.360.085.09
findMateAlignment0.240.000.23
findOverlaps-methods0.450.000.45
findSpliceOverlaps-methods 6.48 0.1423.51
intra-range-methods0.280.000.28
junctions-methods32.45 0.9937.50
mapCoords-methods000
pileLettersAt0.490.000.50
readGAlignments5.960.076.02
sequenceLayer13.56 0.5014.10
setops-methods0.070.000.08
stackStringsFromBam1.500.011.52
summarizeOverlaps-methods 9.26 0.2719.77

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

nameusersystemelapsed
GAlignmentPairs-class1.040.002.59
GAlignments-class0.550.000.54
GAlignmentsList-class3.900.023.91
GappedReads-class0.150.000.14
OverlapEncodings-class0.060.010.07
cigar-utils0.250.000.25
coordinate-mapping-methods9.450.259.71
coverage-methods0.640.080.72
encodeOverlaps-methods0.030.000.03
findCompatibleOverlaps-methods1.570.031.61
findMateAlignment0.220.000.22
findOverlaps-methods0.520.000.51
findSpliceOverlaps-methods6.030.116.15
intra-range-methods0.220.000.22
junctions-methods31.01 1.3432.37
mapCoords-methods000
pileLettersAt0.560.000.56
readGAlignments4.900.084.99
sequenceLayer13.91 0.5914.51
setops-methods0.110.000.11
stackStringsFromBam2.420.002.42
summarizeOverlaps-methods 8.22 0.0820.45