DEGseq 1.14.0
Likun Wang
| 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/DEGseq | | 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 |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DEGseq.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 'DEGseq/DESCRIPTION' ... OK
* this is package 'DEGseq' version '1.14.0'
* 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 'DEGseq' can be installed ... [6s/9s] OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
extdata 5.3Mb
* 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 ... 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 line endings in Makefiles ... 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 ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
samWrapper 8.072 0.564 8.818
DEGexp2 6.698 0.320 7.215
* 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/DEGseq.Rcheck/00check.log'
for details.
* installing *source* package 'DEGseq' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getGeneExp.cpp -o getGeneExp.o
getGeneExp.cpp:101:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(name2);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
getGeneExp.cpp:129:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(filename);
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getGeneExp.cpp:166:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int pos = str.find_first_of(delimiters, lastPos+1);
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getGeneExp.cpp:175:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens.push_back(str.substr(lastPos+1, str.size()-lastPos-1));
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getGeneExp.cpp:175:67: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tokens.push_back(str.substr(lastPos+1, str.size()-lastPos-1));
˜^˜˜˜˜˜˜
getGeneExp.cpp:180:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens.push_back(str.substr(lastPos+1, pos - lastPos-1));
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getGeneExp.cpp:180:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tokens.push_back(str.substr(lastPos+1, pos - lastPos-1));
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getGeneExp.cpp:184:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pos=str.find_first_of(delimiters, lastPos+1);
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getGeneExp.cpp:164:36: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int lastPos = skip_empty ? str.find_first_not_of(delimiters, 0) : 0;
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getGeneExp.cpp:166:19: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int pos = str.find_first_of(delimiters, lastPos+1);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getGeneExp.cpp:184:17: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
pos=str.find_first_of(delimiters, lastPos+1);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getGeneExp.cpp:523:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int end = atoi(exonEnd[iter].c_str());
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getGeneExp.cpp:590:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((!(one_read < exons[pos]))&&(one_read < exons[pos+1])){
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getGeneExp.cpp:590:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((!(one_read < exons[pos]))&&(one_read < exons[pos+1])){
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getGeneExp.cpp:592:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
}else if(one_read < exons[pos]){
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getGeneExp.cpp:595:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
}else if(!(one_read < exons[pos+1])){
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getGeneExp.cpp:615:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exons[pos].chr < one_read.chr){
˜˜˜˜˜ ^˜˜
getGeneExp.cpp:618:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exons[pos].chr > one_read.chr){
˜˜˜˜˜ ^˜˜
getGeneExp.cpp:622:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exons[pos].start + maxExonLen[one_read.chr] < one_read.start){
˜˜˜˜˜ ^˜˜
getGeneExp.cpp:625:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((needSameStrand==true)&&(exons[pos].strand != one_read.strand)){
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getGeneExp.cpp:629:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(one_read.overlap(exons[pos])+0.001 >= overLen){
˜˜˜˜˜ ^˜˜
getGeneExp.cpp:630:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
geneNames.push_back(exons[pos].geneName);
˜˜˜˜˜ ^˜˜
getGeneExp.cpp:582:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int tail=exons.size()-1;
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getGeneExp.cpp:900:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int exon_num = exons.size();
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
24 warnings 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 DEGseq.so getGeneExp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DEGseq.Rcheck/DEGseq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEGseq)