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Last data update: 2014.03.03 |
WhopGenome
Package: WhopGenome Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'WhopGenome' ...
** package 'WhopGenome' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_vcf.cpp -o w_vcf.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c t_main.cpp -o t_main.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c faidx_ifc.cpp -o faidx_ifc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_snpmat_diplo.cpp -o w_snpmat_diplo.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_snpmat_int.cpp -o w_snpmat_int.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_snpmat_str.cpp -o w_snpmat_str.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_snpmat_fnc.cpp -o w_snpmat_fnc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_filtering.cpp -o w_filtering.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_read.cpp -o w_read.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_rsupport.cpp -o w_rsupport.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_tools.cpp -o w_tools.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_dataframe.cpp -o w_dataframe.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_codemat.cpp -o w_codemat.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_main.cpp -o w_main.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_region.cpp -o w_region.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c w_samples.cpp -o w_samples.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c t_region.cpp -o t_region.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c t_info.cpp -o t_info.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c t_read.cpp -o t_read.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c t_Rifc.cpp -o t_Rifc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c readdnapp.cpp -o readdnapp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/bedidx.c -o tabix/bedidx.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/bgzf.c -o tabix/bgzf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/index.c -o tabix/index.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/knetfile.c -o tabix/knetfile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/kstring.c -o tabix/kstring.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/razf.c -o tabix/razf.o
tabix/razf.c: In function 'razf_flush':
tabix/razf.c:233:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
tabix/razf.c:246:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
tabix/razf.c: In function '_razf_write':
tabix/razf.c:213:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
tabix/razf.c: In function 'razf_open_r':
tabix/razf.c:432:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &end, sizeof(int64_t));
^
tabix/razf.c:440:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &end, sizeof(int64_t));
^
tabix/razf.c: In function 'load_zindex':
tabix/razf.c:134:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, &rz->index->size, sizeof(int));
^
tabix/razf.c:143:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
^
tabix/razf.c:149:2: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
^
tabix/razf.c: In function 'razf_close':
tabix/razf.c:825:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->in, sizeof(int64_t));
^
tabix/razf.c:826:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &rz->out, sizeof(int64_t));
^
tabix/razf.c:829:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &v64, sizeof(int64_t));
^
tabix/razf.c:831:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, &v64, sizeof(int64_t));
^
tabix/razf.c: In function 'razf_end_flush':
tabix/razf.c:270:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
tabix/razf.c: In function 'save_zindex':
tabix/razf.c:106:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
if(is_be) write(fd, &rz->index->size, sizeof(int));
^
tabix/razf.c:109:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^
tabix/razf.c:116:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
^
tabix/razf.c:117:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabix/faidx.c -o tabix/faidx.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o WhopGenome.so w_vcf.o t_main.o faidx_ifc.o w_snpmat_diplo.o w_snpmat_int.o w_snpmat_str.o w_snpmat_fnc.o w_filtering.o w_read.o w_rsupport.o w_tools.o w_dataframe.o w_codemat.o w_main.o w_region.o w_samples.o t_region.o t_info.o t_read.o t_Rifc.o readdnapp.o tabix/bedidx.o tabix/bgzf.o tabix/index.o tabix/knetfile.o tabix/kstring.o tabix/razf.o tabix/faidx.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/WhopGenome/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'WhopGenome'
finding HTML links ... done
VCF_read_snp_diplo_bial_int_altpresence
html
VCF_snpmat_diplo_bial_geno_filtered html
WhopPkg-package html
bgzf_compress html
fai_build html
fai_close html
fai_open html
fai_query3 html
fai_query5 html
fai_reopen html
tabix_build html
tabix_close html
tabix_getregion html
tabix_open html
tabix_read html
tabix_reopen html
tabix_restartregion html
tabix_setregion html
vcf_addfilter html
vcf_buildindex html
vcf_clearfilters html
vcf_close html
vcf_countSNPs html
vcf_describefilters html
vcf_getChrom html
vcf_getcontignames html
vcf_getfieldnames html
vcf_getheaderline html
vcf_getnumcontigs html
vcf_getregion html
vcf_isINDEL html
vcf_isSNP html
vcf_open html
vcf_parseNextSNP html
vcf_readLineDF html
vcf_readLineRaw html
vcf_readLineVec html
vcf_reopen html
vcf_restartregion html
vcf_rule.disable html
vcf_rule.setaction html
vcf_rule.setcolumn html
vcf_rule.setcomparison html
vcf_rule.setfield html
vcf_rule.setrefvalues html
vcf_selectsamples html
vcf_setregion html
vcf_valid html
whop.eg.Organism html
whop.eg.abbrevForOrganism html
whop.eg.chromosome html
whop.eg.eg_RevLookup html
whop.eg.eg_lookup html
whop.eg.eg_lookupAll html
whop.eg.eg_lookupSingle html
whop.eg.enzyme html
whop.eg.fromAccnum html
whop.eg.fromAlias html
whop.eg.fromEnsembl html
whop.eg.fromEnsemblProt html
whop.eg.fromEnsemblTrans html
whop.eg.fromEnzyme html
whop.eg.fromGO html
whop.eg.fromGO2AllEgs html
whop.eg.fromOmim html
whop.eg.fromPath html
whop.eg.fromPmid html
whop.eg.fromRefseq html
whop.eg.fromUnigene html
whop.eg.fromUniprot html
whop.eg.genename html
whop.eg.goIds html
whop.eg.installdb html
whop.eg.keggpathways html
whop.eg.load_orgdb html
whop.eg.orgdb_loaded html
whop.eg.region html
whop.eg.selectOrganism html
whop.eg.toAccnum html
whop.eg.toAlias html
whop.eg.toEnsembl html
whop.eg.toEnsemblProt html
whop.eg.toEnsemblTrans html
whop.eg.toEnzyme html
whop.eg.toGO html
whop.eg.toOmim html
whop.eg.toPath html
whop.eg.toPmid html
whop.eg.toRefseq html
whop.eg.toUnigene html
whop.eg.toUniprot html
whop.go.all_genes_for_term html
whop.go.connect html
whop.go.goid_like html
whop.go.is_obsolete_byid html
whop.go.is_obsolete_byname html
whop.go.load html
whop.go.match html
whop.go.term_ancestors html
whop.go.term_ancestors_similar html
whop.go.term_children html
whop.go.term_synonyms html
whop.go.terms_match html
whop.kegg.pathway_url html
whop.ped.daughtersOf html
whop.ped.entriesOf html
whop.ped.familyOf html
whop.ped.fathers html
whop.ped.females html
whop.ped.fromPop html
whop.ped.load html
whop.ped.males html
whop.ped.mothers html
whop.ped.names html
whop.ped.parentsOf html
whop.ped.save html
whop.ped.siblingsOf html
whop.ped.sonsOf html
whop.ucsc.geneInfo html
whop.ucsc.geneInfoSimilar html
whop.ucsc.genesForRegion html
whop.ucsc.query html
** building package indices
** testing if installed package can be loaded
* DONE (WhopGenome)
Making 'packages.html' ... done
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and