Rsubread 1.16.1
Wei Shi
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rsubread | | Last Changed Rev: 96267 / Revision: 102249 | | Last Changed Date: 2014-10-30 22:19:06 -0700 (Thu, 30 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Rsubread.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsubread’ version ‘1.16.1’
* 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 ... [14s/15s] OK
* checking installed package size ... NOTE
installed size is 23.3Mb
sub-directories of 1Mb or more:
annot 20.5Mb
libs 1.6Mb
* 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 loading without being on the library search path ... 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
createAnnotationFile: no visible global function definition for
‘values’
createAnnotationFile: no visible global function definition for
‘seqnames’
createAnnotationFile: no visible global function definition for
‘strand’
getInBuiltAnnotation: no visible binding for global variable
‘annot.inbuilt’
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 ‘strand’
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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: ‘SNPCalling.o’, ‘build-sam-index.o’, ‘core-indel.o’,
‘core-interface-aligner.o’, ‘core-interface-subjunc.o’, ‘core.o’,
‘input-files.o’, ‘propmapped.o’, ‘readSummary.o’,
‘sorted-hashtable.o’
Found ‘srand’, possibly from ‘srand’ (C)
Objects: ‘SNPCalling.o’, ‘core-indel.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
SNPCalling.c: In function ‘read_tmp_block’:
SNPCalling.c:256:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:275:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:276:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:277:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c aligner.c -o aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
atgcContent.c:71:7: warning: unused variable ‘offset’ [-Wunused-variable]
atgcContent.c:70:7: warning: unused variable ‘readlen’ [-Wunused-variable]
atgcContent.c:68:11: warning: unused variable ‘z’ [-Wunused-variable]
atgcContent.c:67:10: warning: unused variable ‘len’ [-Wunused-variable]
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109:11: warning: unused variable ‘z’ [-Wunused-variable]
atgcContent.c:108:10: warning: unused variable ‘len’ [-Wunused-variable]
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:85:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:151:2: warning: ‘readlen’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
build-sam-index.c: In function ‘transfer_SAM_to_position_table’:
build-sam-index.c:363:47: warning: variable ‘is_anchor_certain’ set but not used [-Wunused-but-set-variable]
build-sam-index.c: In function ‘transform_pillup_to_index’:
build-sam-index.c:125:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o
core-indel.c: In function ‘find_new_indels’:
core-indel.c:1317:9: warning: variable ‘best_j’ set but not used [-Wunused-but-set-variable]
core-indel.c: In function ‘full_indel_alignment’:
core-indel.c:2659:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable]
core-indel.c:2659:30: warning: variable ‘best_left’ set but not used [-Wunused-but-set-variable]
core-indel.c: In function ‘find_potential_ultralong_indels’:
core-indel.c:2764:24: warning: variable ‘best_c2_location’ set but not used [-Wunused-but-set-variable]
core-indel.c: In function ‘finalise_pileup_file_by_debrujin’:
core-indel.c:3478:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3479:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3480:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3042:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3043:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3044:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3121:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3122:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
core-indel.c:3123:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o
core-junction.c: In function ‘search_events_to_back’:
core-junction.c:390:6: warning: variable ‘move_start’ set but not used [-Wunused-but-set-variable]
core-junction.c: In function ‘finalise_explain_CIGAR’:
core-junction.c:1663:23: warning: variable ‘tmp_cigar_exonic’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c core.c -o core.o
core.c: In function ‘print_in_box’:
core.c:89:7: warning: variable ‘is_R_linebreak’ set but not used [-Wunused-but-set-variable]
core.c: In function ‘do_voting’:
core.c:2979:9: warning: variable ‘allsubreads_for_each_gap’ set but not used [-Wunused-but-set-variable]
core.c: In function ‘split_read_files’:
core.c:3308:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
core.c:3310:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
core.c:3339:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
core.c:3340:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
detectionCall.c:176:28: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:214:9: warning: unused variable ‘z’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:117:28: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:152:43: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c:152:6: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
detectionCallAnnotation.c: In function ‘calculateIRGCContent’:
detectionCallAnnotation.c:283:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
detectionCallAnnotation.c:196:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function ‘show_cigar’:
gene-algorithms.c:747:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c:746:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c: In function ‘match_chro_indel’:
gene-algorithms.c:1159:28: warning: variable ‘last_section_indels’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1703:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c: In function ‘final_mapping_quality’:
gene-algorithms.c:2344:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘gvindex_load’:
gene-value-index.c:144:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
index-builder.c: In function ‘scan_gene_index’:
index-builder.c:449:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable]
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1123:9: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c input-files.c -o input-files.o
input-files.c: In function ‘sort_SAM_finalise’:
input-files.c:2188:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2194:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2197:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2203:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2256:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2262:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2266:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c:2269:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
input-files.c: In function ‘geinput_next_char’:
input-files.c:442:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
processExons.c:237:10: warning: unused variable ‘pt’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o
propmapped.c: In function ‘prop_PE’:
propmapped.c:346:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
propmapped.c:349:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
propmapped.c:353:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘readSummary’:
readSummary.c:2706:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable]
readSummary.c:2705:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable]
readSummary.c:2705:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable]
readSummary.c: In function ‘load_feature_info’:
readSummary.c:514:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
removeDupReads.c: In function ‘parse_base_blocks’:
removeDupReads.c:87:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
removeDupReads.c:96:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:43:7: warning: unused variable ‘i’ [-Wunused-variable]
sam2bed.c:40:10: warning: variable ‘tok’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:324:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:325:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:326:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:327:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:336:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:344:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:345:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:346:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:350:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:362:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sambam-file.c:366:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘load_int32’:
sorted-hashtable.c:1216:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘load_int64’:
sorted-hashtable.c:1225:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1236:9: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c:1249:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sorted-hashtable.c:1272:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sorted-hashtable.c:1275:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
sorted-hashtable.c:1278:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.16.1\"" -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sublog.c -o sublog.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.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 mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o sublog.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)