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Hackerzone85
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@hackerzone85-10021
Last seen 6.7 years ago
I have faced problem when trying to installing QuasR from github using install_github()
Installing package into ‘C:/Users/BLAB-2/Documents/R/win-library/3.2’ (as ‘lib’ is unspecified) * installing *source* package 'QuasR' ... ** libs g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c count_junctions.cpp -o count_junctions.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o g++ -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c quantify_methylation.cpp -o quantify_methylation.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o gcc -m32 -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/PROGRA~1/R/R-32~1.4/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/include" -I"C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o g++ -m32 -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbam.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbam.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libbcf.a C:/Users/BLAB-2/Documents/R/win-library/3.2/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/BLAB-2/Documents/R/win-library/3.2/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LC:/PROGRA~1/R/R-32~1.4/bin/i386 -lR installing to C:/Users/BLAB-2/Documents/R/win-library/3.2/QuasR/libs/i386 ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'S4Vectors' 0.8.11 is already loaded, but >= 0.9.25 is required ERROR: lazy loading failed for package 'QuasR' * removing 'C:/Users/BLAB-2/Documents/R/win-library/3.2/QuasR' Warning in install.packages : running command '"C:/PROGRA~1/R/R-32~1.4/bin/i386/R" CMD INSTALL -l "C:\Users\BLAB-2\Documents\R\win-library\3.2" "C:/Users/BLAB-2/Downloads/Compressed/QuasR_1.11.2.tar.gz"' had status 1 Warning in install.packages : installation of package ‘C:/Users/BLAB-2/Downloads/Compressed/QuasR_1.11.2.tar.gz’ had non-zero exit status
sessioninfo:
R version 3.2.4 Revised (2016-03-16 r70336) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq2_1.10.1 RcppArmadillo_0.6.600.4.0 [3] Rcpp_0.12.4 SummarizedExperiment_1.0.2 [5] Biobase_2.30.0 GenomicRanges_1.22.4 [7] GenomeInfoDb_1.6.3 IRanges_2.4.8 [9] S4Vectors_0.8.11 BiocGenerics_0.16.1 [11] BiocInstaller_1.20.1 loaded via a namespace (and not attached): [1] Formula_1.2-1 DBI_0.3.1 ggplot2_2.1.0 [4] geneplotter_1.48.0 genefilter_1.52.1 futile.options_1.0.0 [7] zlibbioc_1.16.0 lattice_0.20-33 RSQLite_1.0.0 [10] foreign_0.8-66 xtable_1.8-2 gridExtra_2.2.1 [13] plyr_1.8.3 tools_3.2.4 BiocParallel_1.4.3 [16] annotate_1.48.0 lambda.r_1.1.7 XVector_0.10.0 [19] futile.logger_1.4.1 scales_0.4.0 nnet_7.3-12 [22] gtable_0.2.0 latticeExtra_0.6-28 cluster_2.0.3 [25] rpart_4.1-10 munsell_0.4.3 grid_3.2.4 [28] XML_3.98-1.4 colorspace_1.2-6 AnnotationDbi_1.32.3 [31] Hmisc_3.17-2 splines_3.2.4 survival_2.38-3 [34] RColorBrewer_1.1-2 acepack_1.3-3.3 locfit_1.5-9.1
