[BioC] compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Starr Hazard [guest]
guest at bioconductor.org
Thu Nov 1 15:48:40 CET 2012
Rcurl now installed in R.2.15.2 but still chocking on IRanges at tzset
cc -std=gnu99 -shared -L/usr/local/lib64 -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -lz -lm
installing to /depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/RCurl/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'close' from package 'base' in package 'RCurl'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RCurl)
#hpcc3:/home/hazards/COMPILE3: /shared/app/R-2.15.2-mpich2i12/bin/R
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'cummeRbund'
also installing the dependencies 'GenomicRanges', 'IRanges', 'Biostrings', 'BSgenome', 'Rsamtools', 'biomaRt', 'AnnotationDbi', 'GenomicFeatures', 'biovizBase', 'rtracklayer', 'Gviz'
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicRanges_1.10.3.tar.gz'
Content type 'application/x-gzip' length 2567958 bytes (2.4 Mb)
opened URL
==================================================
downloaded 2.4 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/IRanges_1.16.3.tar.gz'
Content type 'application/x-gzip' length 699165 bytes (682 Kb)
opened URL
==================================================
downloaded 682 Kb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Biostrings_2.26.2.tar.gz'
Content type 'application/x-gzip' length 1320819 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/BSgenome_1.26.1.tar.gz'
Content type 'application/x-gzip' length 523498 bytes (511 Kb)
opened URL
==================================================
downloaded 511 Kb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Rsamtools_1.10.1.tar.gz'
Content type 'application/x-gzip' length 2111065 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biomaRt_2.14.0.tar.gz'
Content type 'application/x-gzip' length 276758 bytes (270 Kb)
opened URL
==================================================
downloaded 270 Kb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/AnnotationDbi_1.20.2.tar.gz'
Content type 'application/x-gzip' length 3736581 bytes (3.6 Mb)
opened URL
==================================================
downloaded 3.6 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatures_1.10.0.tar.gz'
Content type 'application/x-gzip' length 742114 bytes (724 Kb)
opened URL
==================================================
downloaded 724 Kb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biovizBase_1.6.0.tar.gz'
Content type 'application/x-gzip' length 1025033 bytes (1001 Kb)
opened URL
==================================================
downloaded 1001 Kb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/rtracklayer_1.18.0.tar.gz'
Content type 'application/x-gzip' length 1307339 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Gviz_1.2.0.tar.gz'
Content type 'application/x-gzip' length 1391602 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/cummeRbund_2.0.0.tar.gz'
Content type 'application/x-gzip' length 2327551 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb
* installing *source* package 'IRanges' ...
** libs
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c AEbufs.c -o AEbufs.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c CompressedList_class.c -o CompressedList_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c DataFrame_class.c -o DataFrame_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c GappedRanges_class.c -o GappedRanges_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Grouping_class.c -o Grouping_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Hits_class.c -o Hits_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c IRanges_class.c -o IRanges_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c IRanges_constructor.c -o IRanges_constructor.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c IRanges_utils.c -o IRanges_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c IntervalTree.c -o IntervalTree.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
IntervalTree.c(130): warning #188: enumerated type mixed with another type
Rboolean hit = FALSE; /* already hit current node? */
^
IntervalTree.c(190): warning #188: enumerated type mixed with another type
Rboolean visited = height && p == tree->stack[height-1];
^
IntervalTree.c(227): warning #188: enumerated type mixed with another type
hit = TRUE;
^
IntervalTree.c(240): warning #188: enumerated type mixed with another type
hit = FALSE;
^
IntervalTree.c(250): warning #188: enumerated type mixed with another type
hit = FALSE;
^
IntervalTree.c(496): warning #188: enumerated type mixed with another type
Rboolean visited = height && p == tree->stack[height-1];
^
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c R_init_IRanges.c -o R_init_IRanges.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c RangedData_class.c -o RangedData_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Ranges_comparison.c -o Ranges_comparison.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c RleViews_utils.c -o RleViews_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Rle_class.c -o Rle_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Rle_utils.c -o Rle_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
Rle_utils.c(735): warning #266: function "roundingScale" declared implicitly
q_index = roundingScale(window_len_na,
^
Rle_utils.c(859): warning #266: function "roundingScale" declared implicitly
q_index = roundingScale(window_len_na,
^
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SEXP_utils.c -o SEXP_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SharedDouble_utils.c -o SharedDouble_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SharedInteger_utils.c -o SharedInteger_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SharedRaw_utils.c -o SharedRaw_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SharedVector_class.c -o SharedVector_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SimpleList_class.c -o SimpleList_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c Vector_class.c -o Vector_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
Vector_class.c(95): warning #266: function "UNIMPLEMENTED_TYPE" declared implicitly
UNIMPLEMENTED_TYPE("vector_seqselect", x);
^
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c XDoubleViews_utils.c -o XDoubleViews_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c XRawList_comparison.c -o XRawList_comparison.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c XVectorList_class.c -o XVectorList_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c XVector_class.c -o XVector_class.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c anyMissing.c -o anyMissing.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c common.c -o common.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c compact_bitvector.c -o compact_bitvector.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c coverage.c -o coverage.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c dlist.c -o dlist.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c encode_overlaps.c -o encode_overlaps.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c errabort.c -o errabort.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c hash_utils.c -o hash_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c int_utils.c -o int_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c localmem.c -o localmem.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c memalloc.c -o memalloc.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c rbTree.c -o rbTree.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c safe_arithm.c -o safe_arithm.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c sort_utils.c -o sort_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -std=c99 -c str_utils.c -o str_utils.o
icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
str_utils.c(150): warning #266: function "tzset" declared implicitly
tzset();
^
str_utils.c(152): error: identifier "timezone" is undefined
utc_offset = - (timezone / 3600);
^
compilation aborted for str_utils.c (code 2)
make: *** [str_utils.o] Error 2
ERROR: compilation failed for package 'IRanges'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges'
* installing *source* package 'biomaRt' ...
** R
** inst
Rcurl now installed in R2.15.2
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'biomaRt.Rnw'
** testing if installed package can be loaded
* DONE (biomaRt)
ERROR: dependency 'IRanges' is not available for package 'GenomicRanges'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/GenomicRanges'
ERROR: dependency 'IRanges' is not available for package 'Biostrings'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings'
ERROR: dependency 'IRanges' is not available for package 'AnnotationDbi'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/AnnotationDbi'
ERROR: dependencies 'IRanges', 'GenomicRanges', 'Biostrings' are not available for package 'BSgenome'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/BSgenome'
ERROR: dependencies 'IRanges', 'GenomicRanges', 'Biostrings' are not available for package 'Rsamtools'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Rsamtools'
ERROR: dependencies 'GenomicRanges', 'IRanges', 'Biostrings', 'BSgenome', 'Rsamtools' are not available for package 'rtracklayer'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/rtracklayer'
ERROR: dependencies 'IRanges', 'GenomicRanges', 'AnnotationDbi', 'Biostrings', 'rtracklayer' are not available for package 'GenomicFeatures'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/GenomicFeatures'
ERROR: dependencies 'IRanges', 'GenomicRanges', 'Biostrings', 'Rsamtools', 'GenomicFeatures' are not available for package 'biovizBase'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/biovizBase'
ERROR: dependencies 'IRanges', 'rtracklayer', 'GenomicRanges', 'AnnotationDbi', 'GenomicFeatures', 'BSgenome', 'Biostrings', 'biovizBase' are not available for package 'Gviz'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Gviz'
ERROR: dependencies 'rtracklayer', 'Gviz' are not available for package 'cummeRbund'
* removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/cummeRbund'
The downloaded source packages are in
'/tmp/RtmphfHuxG/downloaded_packages'
There were 11 warnings (use warnings() to see them)
-- output of sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
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