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Package 169/671HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.6.0
Erik Wright
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DECIPHER
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: DECIPHER
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DECIPHER_1.6.0.tar.gz
StartedAt: 2013-05-01 04:23:05 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 04:27:18 -0700 (Wed, 01 May 2013)
EllapsedTime: 252.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.6.0'
* 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 ... [14s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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
DB2FASTA: warning in writeXStringSet(myDNAStringSet, file = file,
  append = append): partial argument match of 'file' to 'filepath'
CreateChimeras: no visible binding for global variable 's1'
CreateChimeras: no visible binding for global variable 'd'
CreateChimeras: no visible binding for global variable 'myName'
* 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 for portable 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 examples ... [107s/112s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
TileSeqs 88.454  4.649  95.316
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package 'DECIPHER' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c CalculateDeltaG.c -o CalculateDeltaG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ClusterML.c -o ClusterML.o
ClusterML.c:269:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *Ls = (double *) R_alloc(length*8, sizeof(double));
                                ˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
ClusterML.c:270:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *widths = (int *) R_alloc(length, sizeof(int));
                              ˜˜˜˜˜˜˜ ^˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c:202:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        size = sqrt(length(x)); // square distance matrix dimension
             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ClusterNJ.c:207:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *dMatrix = (double *) R_alloc(size*size, sizeof(double)); // final row & col contain cluster numbers
                                     ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
ClusterNJ.c:266:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j,minR,minC,minH) schedule(guided)
                        ^
ClusterNJ.c:276:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp critical
                                ^
ClusterNJ.c:436:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterNJ.c:448:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterNJ.c:486:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                        *rPercentComplete = floor(100*soFar/total);
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c:131:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        size = sqrt(length(x)); // square distance matrix dimension
             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ClusterUPGMA.c:136:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *dMatrix = (double *) R_alloc(size*size, sizeof(double)); // final row & col contain cluster numbers
                                     ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
ClusterUPGMA.c:183:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j,minR,minC,minH) schedule(guided)
                        ^
ClusterUPGMA.c:193:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp critical
                                ^
ClusterUPGMA.c:343:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterUPGMA.c:355:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterUPGMA.c:393:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                        *rPercentComplete = floor(100*soFar/total);
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c CommonGaps.c -o CommonGaps.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ConsensusSequence.c -o ConsensusSequence.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c:174:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp parallel for private(j,x_j,seqLength_j,start,end) schedule(guided)
                                ^
DistanceMatrix.c:213:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                                *rPercentComplete = floor(100*(double)soFar/((x_length - 1)*x_length+(x_length - 1)));
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MultiMatch.c -o MultiMatch.o
MultiMatch.c:189:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i, j) schedule(guided)
                ^
MultiMatch.c:215:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i, j) schedule(guided)
                ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_init_decipher.c -o R_init_decipher.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ReplaceChars.c -o ReplaceChars.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c:46:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i,j,lp,lt,l,mm,count,end,gaps,probe,target) schedule(guided)
                ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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
Add2DB0.8300.0260.934
BrowseDB0.2620.0070.312
BrowseSequences0.1270.0090.153
CalculateEfficiencyArray0.4520.0170.581
CalculateEfficiencyPCR0.0320.0080.056
ConsensusSequence0.0220.0040.027
CreateChimeras1.8000.0782.097
DB2FASTA0.0350.0200.116
DesignPrimers0.0110.0030.014
DistanceMatrix0.0240.0060.029
FindChimeras0.6740.0150.731
FormGroups0.0700.0060.429
IdClusters0.0590.0060.077
IdConsensus2.2650.0732.761
IdLengths0.0600.0050.069
IdentifyByRank0.0490.0060.065
SearchDB0.2470.0070.295
Seqs2DB0.6610.0160.798
TerminalChar0.0500.0060.068
TileSeqs88.454 4.64995.316
deltaGrules0.0330.0150.048