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I am trying to install IRanges in R 3.3 with bioconductor 3.3.
The error message is here:
> source("https://bioconductor.org/biocLite.R") Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help > biocLite("IRanges") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘IRanges’ trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.6.1.tar.gz' Content type 'application/x-gzip' length 475440 bytes (464 KB) ================================================== downloaded 464 KB
* installing *source* package ‘IRanges’ ... ** libs gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c CompressedList_class.c -o CompressedList_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c GappedRanges_class.c -o GappedRanges_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c Grouping_class.c -o Grouping_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c IRanges_class.c -o IRanges_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c NCList.c -o NCList.o NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function] static const NCList *next_top_down(const NCList *nclist) ^ NCList.c:1184:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function] static void NCList_get_y_overlaps_rec(const NCList *x_nclist, ^ NCList.c: In function ‘NCList_find_overlaps_in_groups’: NCList.c:1553:7: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized] SEXP ans; ^ gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c Ranges_class.c -o Ranges_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c Ranges_comparison.c -o Ranges_comparison.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c RleViews_utils.c -o RleViews_utils.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c SimpleRangesList_class.c -o SimpleRangesList_class.o gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c coverage_methods.c -o coverage_methods.o coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’: coverage_methods.c:503:28: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (*out_ranges_are_tiles && x_end != cvg_len) ^ coverage_methods.c:419:21: note: ‘x_end’ was declared here i, j, x_start, x_end, shift_elt, tmp; ^ gcc -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o inter_range_methods.c: In function ‘reduce_ranges’: inter_range_methods.c:165:5: warning: ‘revmap_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized] IntAE_insert_at(revmap_elt, ^ inter_range_methods.c:154:11: warning: ‘delta’ may be used uninitialized in this function [-Wmaybe-uninitialized] delta += gapwidth; ^ inter_range_methods.c:154:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized] inter_range_methods.c:156:14: warning: ‘max_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] width_inc = end_j - max_end; ^ inter_range_methods.c:131:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (append_or_drop) { ^ gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/usr/lib64/R/lib -lR installing to /home/jl/R/x86_64-redhat-linux-gnu-library/3.3/IRanges/libs ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’ Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : methods can add arguments to the generic ‘NSBS’ only if '...' is an argument to the generic Error : unable to load R code in package ‘IRanges’ ERROR: lazy loading failed for package ‘IRanges’ * removing ‘/home/jl/R/x86_64-redhat-linux-gnu-library/3.3/IRanges’
The downloaded source packages are in ‘/tmp/RtmpnK0JTG/downloaded_packages’ Old packages: 'AnnotationDbi', 'biomaRt', 'Biostrings', 'BSgenome', 'CNEr', 'DirichletMultinomial', 'GenomeInfoDb', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges', 'IRanges', 'Rsamtools', 'rtracklayer', 'ShortRead', 'SummarizedExperiment', 'TFBSTools', 'XVector' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘IRanges’ had non-zero exit status
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora 23 (Workstation Edition)
locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] BiocInstaller_1.22.3
loaded via a namespace (and not attached): [1] tools_3.3.1