BioC 3.3: CHECK report for Rsubread on oaxaca
This page was generated on 2016-10-13 12:57:40 -0700 (Thu, 13 Oct 2016).
Rsubread 1.22.3
Wei Shi
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Rsubread | | Last Changed Rev: 119703 / Revision: 122332 | | Last Changed Date: 2016-07-27 21:22:55 -0700 (Wed, 27 Jul 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
| Package: Rsubread |
| Version: 1.22.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.22.3.tar.gz |
| StartedAt: 2016-10-13 05:58:00 -0700 (Thu, 13 Oct 2016) |
| EndedAt: 2016-10-13 05:58:43 -0700 (Thu, 13 Oct 2016) |
| EllapsedTime: 43.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.22.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘1.22.3’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 30.4Mb
sub-directories of 1Mb or more:
annot 28.5Mb
* checking package directory ... OK
* checking ‘build’ 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 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
.findCommonVariants_inner: no visible global function definition for
‘read.delim’
atgcContent: no visible global function definition for ‘read.csv’
createAnnotationFile: no visible global function definition for ‘is’
createAnnotationFile: no visible global function definition for
‘values’
createAnnotationFile: no visible global function definition for
‘seqnames’
createAnnotationFile: no visible global function definition for ‘start’
createAnnotationFile: no visible global function definition for ‘end’
createAnnotationFile: no visible global function definition for
‘strand’
detectionCall: no visible global function definition for ‘read.delim’
detectionCall: no visible global function definition for ‘lowess’
detectionCall: no visible global function definition for ‘approxfun’
detectionCall: no visible global function definition for ‘ppois’
detectionCall: no visible global function definition for ‘runif’
detectionCall: no visible global function definition for ‘dpois’
detectionCall: no visible global function definition for ‘pdf’
detectionCall: no visible global function definition for ‘density’
detectionCall: no visible global function definition for ‘dev.off’
featureCounts: no visible global function definition for ‘write.table’
featureCounts: no visible global function definition for ‘read.delim’
findCommonVariants: no visible global function definition for
‘read.delim’
getInBuiltAnnotation: no visible binding for global variable
‘annot.inbuilt’
getInBuiltAnnotation: no visible global function definition for
‘read.delim’
processExons: no visible global function definition for ‘read.delim’
processExons: no visible global function definition for ‘write.table’
propmapped: no visible global function definition for ‘read.delim’
qualityScores: no visible global function definition for ‘read.csv’
write.Rsubread: no visible global function definition for ‘is’
write.Rsubread: no visible global function definition for ‘values’
write.Rsubread: no visible global function definition for ‘seqnames’
write.Rsubread: no visible global function definition for ‘start’
write.Rsubread: no visible global function definition for ‘end’
write.Rsubread: no visible global function definition for ‘strand’
Undefined global functions or variables:
annot.inbuilt approxfun density dev.off dpois end is lowess pdf ppois
read.csv read.delim runif seqnames start strand values write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("methods", "is")
importFrom("stats", "approxfun", "density", "dpois", "end", "lowess",
"ppois", "runif", "start")
importFrom("utils", "read.csv", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rsubread/libs/Rsubread.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Objects: ‘HelperFunctions.o’, ‘build-sam-index.o’, ‘core.o’,
‘sorted-hashtable.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Objects: ‘HelperFunctions.o’, ‘core-indel.o’, ‘core.o’,
‘propmapped.o’
File ‘Rsubread/libs/Rsubread.so’:
Found non-API call to R: ‘R_CStackLimit’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out:
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Darwin.
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c HelperFunctions.c -o HelperFunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c R_wrapper.c -o R_wrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c SNPCalling.c -o SNPCalling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c aligner.c -o aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c atgcContent.c -o atgcContent.o
atgcContent.c:68:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
atgcContent.c:71:7: warning: unused variable 'offset' [-Wunused-variable]
int offset;
^
atgcContent.c:70:7: warning: unused variable 'readlen' [-Wunused-variable]
int readlen;
^
atgcContent.c:67:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
atgcContent.c:73:7: warning: unused variable 'data_ready' [-Wunused-variable]
int data_ready=1;
^
atgcContent.c:109:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
atgcContent.c:108:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-bigtable.c -o core-bigtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-indel.c -o core-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-junction.c -o core-junction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c core.c -o core.o
core.c:2645:25: warning: unused variable 'current_result' [-Wunused-variable]
mapping_result_t *current_result = current_realignment_result -> mapping_result;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c detectionCall.c -o detectionCall.o
detectionCall.c:176:28: warning: unused variable 'read_entrezid' [-Wunused-variable]
int read_start, read_end, read_entrezid, read_n, read_gc, read_at;
^
detectionCall.c:214:9: warning: unused variable 'z' [-Wunused-variable]
size_t z;
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:117:28: warning: unused variable 'read_length' [-Wunused-variable]
int read_start, read_end, read_length;
^
detectionCallAnnotation.c:152:6: warning: unused variable 'read_entrezid' [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c:152:43: warning: unused variable 'read_length' [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-align.c -o exon-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c fullscan.c -o fullscan.o
fullscan.c:49:58: warning: passing 'unsigned int *' to parameter of type 'int *' converts between pointers to integer types with different sign [-Wpointer-sign]
locate_gene_position(pos, &_global_offsets, &chro_name, &chro_pos);
^˜˜˜˜˜˜˜˜
./gene-algorithms.h:35:103: note: passing argument to parameter 'pos' here
int locate_gene_position(unsigned int linear, const gene_offset_t* offsets , char ** chro_name, int * pos);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c fusion-align.c -o fusion-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c gene-algorithms.c -o gene-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c gene-value-index.c -o gene-value-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c hashtable.c -o hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c index-builder.c -o index-builder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c input-files.c -o input-files.o
input-files.c:2374:43: warning: too many arguments in call to 'SAM_pairer_warning_file_open_limit'
SAM_pairer_warning_file_open_limit(pairer);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c interval_merge.c -o interval_merge.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c long-hashtable.c -o long-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c mergeVCF.c -o mergeVCF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c processExons.c -o processExons.o
processExons.c:237:10: warning: unused variable 'pt' [-Wunused-variable]
char *pt = strcpy(gene_array[gene_pos].chr_array[current_chr_index].id,chr_id);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c propmapped.c -o propmapped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c qualityScores.c -o qualityScores.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c read-repair.c -o read-repair.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c readSummary.c -o readSummary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c removeDupReads.c -o removeDupReads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c sam2bed.c -o sam2bed.o
sam2bed.c:43:7: warning: unused variable 'i' [-Wunused-variable]
int i, readlen, chr_start, chr_end, flag, mqs;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c sambam-file.c -o sambam-file.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c seek-zlib.c -o seek-zlib.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.22.3\"" -fPIC -Wall -mtune=core2 -g -O2 -c sublog.c -o sublog.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck/Rsubread/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 (Rsubread)
Rsubread.Rcheck/Rsubread-Ex.timings:
| name | user | system | elapsed
|
| align | 1.907 | 1.820 | 3.728 |
|
| buildindex | 0.445 | 0.724 | 1.170 |
|
| createAnnotationFile | 0.001 | 0.000 | 0.001 |
|
| featureCounts | 0.001 | 0.000 | 0.001 |
|
| findCommonVariants | 0 | 0 | 0 |
|
| getInBuiltAnnotation | 3.108 | 0.050 | 3.160 |
|
| propmapped | 2.270 | 2.096 | 4.371 |
|
| qualityScores | 0.079 | 0.003 | 0.083 |
|