Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

Package 424/479HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.11.23
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 56598 / Revision: 56603
Last Changed Date: 2011-07-06 15:55:59 -0700 (Wed, 06 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ WARNINGS ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ShortRead
Version: 1.11.23
Command: mkdir ShortRead.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.11.23.tar.gz >ShortRead-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=ShortRead.buildbin-libdir --install="check:ShortRead-install.out" --force-multiarch --no-vignettes --timings ShortRead_1.11.23.tar.gz && mv ShortRead.buildbin-libdir/* ShortRead.Rcheck/ && rmdir ShortRead.buildbin-libdir
StartedAt: 2011-07-07 06:15:57 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 06:21:51 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 353.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 3

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.11.23'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'Rmpi' 'multicore'
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... WARNING
Found the following significant warnings:
  Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
See 'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.coverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible global function definition for
  '.getData<-'
.multicoverage_viewer: no visible binding for global variable 'lv'
.multicoverage_viewer: no visible binding for global variable 'group'
.multicoverage_viewer: no visible binding for global variable 'sv'
.plotCycleBaseCall: no visible binding for global variable 'Base'
.plotNucleotideCount: no visible binding for global variable
  'Nucleotide'
.plotReadCount: no visible binding for global variable 'Census'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpwlR1FT/R.INSTALL6c002673/ShortRead/man/Snapshot-class.Rd':
  'Snapshot-class'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GappedReads' 'qname' 'qseq' 'readGappedReads'
Undocumented S4 classes:
  'AssayData' 'GappedReads' 'Snapshot' 'trellis'
Undocumented S4 methods:
  generic 'SnapshotFunctionList' and siglist 'SnapshotFunction'
  generic '[' and siglist 'GappedReads,ANY,ANY'
  generic 'c' and siglist 'GappedReads'
  generic 'narrow' and siglist 'GappedReads'
  generic 'qname' and siglist 'GappedReads'
  generic 'qseq' and siglist 'GappedReads'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'ShortRead_unit_tests.R'
 OK
** running tests for arch 'x64'
  Running 'ShortRead_unit_tests.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings, see
  'D:/biocbld/bbs-2.9-bioc/meat/ShortRead.Rcheck/00check.log'
for details

ShortRead.Rcheck/00install.out:


install for i386

* installing *source* package 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: RColorBrewer
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Overview.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.11.23.zip

* DONE (ShortRead)

ShortRead.Rcheck/ShortRead-Ex.timings:

nameusersystemelapsed
AlignedRead-class0.560.240.80
BAMQA-class000
BowtieQA-class000
ExperimentPath-class000
FastqQA-class000
Intensity-class0.570.000.67
MAQMapQA-class000
QA-class000
QualityScore-class000
QualityScore000
RochePath-class000
RocheSet-class000
RtaIntensity-class0.080.000.08
RtaIntensity0.050.000.05
SRFilter-class000
SRFilterResult-class0.070.000.08
SRSet-class000
SRUtil-class000
Sampler-class0.340.120.47
ShortRead-class0.080.000.08
ShortReadQ-class0.420.280.70
Snapshot-class1.730.001.73
SnapshotFunction-class000
SolexaExportQA-class000
SolexaIntensity-class0.160.000.16
SolexaPath-class0.20.30.5
SolexaSet-class0.100.000.09
SpTrellis-class000
accessors000
alphabetByCycle0.200.250.45
clean000
countLines0.030.000.03
deprecated000
dustyScore0.360.280.64
polyn000
qa0.870.361.24
readAligned0.720.541.26
readBaseQuality0.060.080.14
readFasta0.080.000.07
readFastq0.430.531.08
readIntensities0.100.020.11
readPrb0.070.000.08
readQseq0.100.140.23
readXStringColumns0.500.430.94
renew0.180.130.31
report000
srFilter0.580.310.89
srapply000
srdistance0.310.130.44
srduplicated0.240.280.51
tables0.230.220.45
trimTails000