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 

BioC 2.13: CHECK report for DECIPHER on zin1

This page was generated on 2014-04-05 09:48:10 -0700 (Sat, 05 Apr 2014).

Package 192/750HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.8.0
Erik Wright
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/DECIPHER
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.8.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.8.0.tar.gz
StartedAt: 2014-04-05 00:40:53 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:45:48 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 295.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DECIPHER.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘DECIPHER’ can be installed ... [11s/11s] 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:
  ‘Biostrings’ ‘parallel’ ‘RSQLite’ ‘IRanges’ ‘stats’ ‘XVector’
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
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘XVector’ ‘parallel’ ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘XVector’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DECIPHERing.Rnw’, ‘DesignMicroarray.Rnw’, ‘DesignPrimers.Rnw’,
  ‘DesignProbes.Rnw’, ‘FindChimeras.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [521s/202s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
AlignSeqs     437.472  0.984 154.745
AlignProfiles  40.174  0.160  15.872
TileSeqs       11.893  0.076  12.440
DesignArray    10.057  0.060   4.521
Array2Matrix    9.852  0.060   4.465
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for ‘dH_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for ‘dS_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for ‘dH_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for ‘dS_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for ‘dH_RR[0]’) [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for ‘dS_RR[0]’) [-Wmissing-braces]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:281:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: ‘minC’ was declared here
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:198:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
ClusterUPGMA.c:197:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for ‘NN[0]’) [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for ‘PM[0]’) [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for ‘sMM[0]’) [-Wmissing-braces]
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:829:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
DesignProbes.c:829:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -shared -L/usr/local/lib -o DECIPHER.so AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.3920.0080.404
AlignProfiles40.174 0.16015.872
AlignSeqs437.472 0.984154.745
Array2Matrix9.8520.0604.465
BrowseDB0.0360.0040.042
BrowseSequences0.0760.0040.095
CalculateEfficiencyArray0.0280.0120.042
CalculateEfficiencyFISH0.0120.0000.015
CalculateEfficiencyPCR0.0160.0000.015
ConsensusSequence0.0120.0000.013
CreateChimeras1.8600.0521.528
DB2FASTA0.0520.0160.103
DesignArray10.057 0.060 4.521
DesignPrimers0.0040.0000.004
DesignProbes0.0040.0000.005
DistanceMatrix0.0600.0160.052
FindChimeras0.4120.0080.422
FormGroups0.0400.0000.042
IdClusters0.5360.0240.226
IdConsensus1.3920.0361.432
IdLengths0.0320.0040.035
IdentifyByRank0.0280.0080.035
MODELS0.0000.0000.023
MaskAlignment0.9600.0761.040
NNLS0.1760.0200.093
SearchDB0.0280.0000.028
Seqs2DB0.3640.0080.375
TerminalChar0.0280.0040.032
TileSeqs11.893 0.07612.440
deltaGrules0.0040.0080.014