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Package 160/389HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicRanges 1.0.9
Biocore Team c/o BioC user list
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GenomicRanges
Last Changed Rev: 49071 / Revision: 49923
Last Changed Date: 2010-08-27 19:20:48 -0700 (Fri, 27 Aug 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GenomicRanges
Version: 1.0.9
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GenomicRanges_1.0.9.tar.gz
StartedAt: 2010-10-04 18:24:22 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:26:38 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 135.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomicRanges.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/GenomicRanges.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.0.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GenomicRanges' can be installed ... OK
* 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
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'GenomicRanges_unit_tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

GenomicRanges.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'GenomicRanges' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"   -I"E:/biocbld/bbs-2.6-bioc/R/library/IRanges/include"      -O3 -Wall  -std=gnu99 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:500: warning: 'OPL' may be used uninitialized in this function
cigar_utils.c:500: note: 'OPL' was declared here
cigar_utils.c:501: warning: 'OP' may be used uninitialized in this function
cigar_utils.c:501: note: 'OP' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:340: warning: 'OPL' may be used uninitialized in this function
cigar_utils.c:340: note: 'OPL' was declared here
cigar_utils.c:341: warning: 'OP' may be used uninitialized in this function
cigar_utils.c:341: note: 'OP' was declared here
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:897: warning: 'width' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_qwidth2':
cigar_utils.c:861: warning: 'qwidth' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/GenomicRanges.Rcheck/GenomicRanges/libs
  ... done
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

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

    Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
    rbind, rep.int, table

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GenomicRanges)

GenomicRanges.Rcheck/GenomicRanges-Ex.timings:

nameusersystemelapsed
GRanges-class0.750.000.75
GRanges-findOverlaps2.210.002.22
GRanges-setops0.950.020.97
GRangesList-class0.620.000.63
GappedAlignments-class2.960.033.11
cigar-utils0.550.010.56
seqnames0.280.020.42
strand000