"rtracklayer" compilation error
1
0
Entering edit mode
Biologist ▴ 110
@biologist-9801
Last seen 4.0 years ago

I wanted to install minfiData package and for that it need "rtacklayer". When I installed it Im getting the following error.

> biocLite("rtracklayer")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘rtracklayer’
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/rtracklayer_1.32.1.tar.gz'
Content type 'unknown' length 1378505 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... no
checking for OPENSSL... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c readGFF.c -o readGFF.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
         fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */
              ^
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c handlers.c -o handlers.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c utils.c -o utils.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘reverseComplementSlashSeparated’:
ucsc/dnautil.c:496:5: warning: implicit declaration of function ‘isAllNt’ [-Wimplicit-function-declaration]
     if (isAllNt(allele, alLen))
     ^
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:10: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
     write(STDERR_FILENO, errMsg, strlen(errMsg));
          ^
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/export/home/vkancher/src/R-3.3.0/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/export/home/vkancher/src/R-3.3.0/library/S4Vectors/include" -I"/export/home/vkancher/src/R-3.3.0/library/IRanges/include" -I"/export/home/vkancher/src/R-3.3.0/library/XVector/include"   -fpic  -g -O2  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c:7:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
                  ^
compilation terminated.
make: *** [ucsc/zlibFace.o] Error 1
ERROR: compilation failed for package ‘rtracklayer’
* removing ‘/export/home/vkancher/src/R-3.3.0/library/rtracklayer’
* restoring previous ‘/export/home/vkancher/src/R-3.3.0/library/rtracklayer’

The downloaded source packages are in
        ‘/tmp/RtmpuCd0Wu/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'rtracklayer'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status

rtracklayer • 1.3k views
ADD COMMENT
0
Entering edit mode

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] BiocInstaller_1.22.3
 [2] matrixStats_0.50.2
 [3] missMethyl_1.6.2
 [4] RColorBrewer_1.1-2
 [5] limma_3.28.14
 [6] IlluminaHumanMethylation450kmanifest_0.4.0
 [7] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [8] minfi_1.18.2
 [9] bumphunter_1.12.0
[10] locfit_1.5-9.1
[11] iterators_1.0.8
[12] foreach_1.4.3
[13] Biostrings_2.40.2
[14] XVector_0.12.0
[15] SummarizedExperiment_1.2.3
[16] GenomicRanges_1.24.2
[17] GenomeInfoDb_1.8.1
[18] IRanges_2.6.1
[19] S4Vectors_0.10.1
[20] lattice_0.20-33
[21] Biobase_2.32.0
[22] BiocGenerics_0.18.0
[23] stringr_1.0.0

loaded via a namespace (and not attached):
 [1] mclust_5.2              base64_2.0              Rcpp_0.12.5
 [4] Rsamtools_1.24.0        digest_0.6.9            R6_2.1.2
 [7] plyr_1.8.4              chron_2.3-47            RSQLite_1.0.0
[10] httr_1.2.1              zlibbioc_1.18.0         GenomicFeatures_1.24.3
[13] data.table_1.9.6        annotate_1.50.0         Matrix_1.2-6
[16] preprocessCore_1.34.0   splines_3.3.0           statmod_1.4.24
[19] BiocParallel_1.6.2      RCurl_1.95-4.8          biomaRt_2.28.0
[22] rtracklayer_1.32.0      multtest_2.28.0         ruv_0.9.6
[25] pkgmaker_0.22           openssl_0.9.4           GEOquery_2.38.4
[28] quadprog_1.5-5          codetools_0.2-14        XML_3.98-1.4
[31] reshape_0.8.5           GenomicAlignments_1.8.3 MASS_7.3-45
[34] bitops_1.0-6            grid_3.3.0              nlme_3.1-128
[37] xtable_1.8-2            registry_0.3            DBI_0.4-1
[40] magrittr_1.5            stringi_1.1.1           genefilter_1.54.2
[43] doRNG_1.6               nor1mix_1.2-1           org.Hs.eg.db_3.3.0
[46] siggenes_1.46.0         tools_3.3.0             illuminaio_0.14.0
[49] rngtools_1.2.4          survival_2.39-5         methylumi_2.18.2
[52] AnnotationDbi_1.34.3    colorspace_1.2-6        beanplot_1.2

ADD REPLY
1
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg

Looks like you need to install the development version of the zlib system library.  Give this a try in the command line, and then try install the package again:

sudo apt-get install zlib1g-dev
ADD COMMENT
0
Entering edit mode

I *think* that this should have been available when R was built, so perhaps worth understanding why they are no longer available.

ADD REPLY
0
Entering edit mode

I think you're right Martin.  That library is listed as a dependency if you're installing from an Ubuntu repository:

apt-cache depends r-base-core | grep zlib
  Depends: zlib1g

 

ADD REPLY
0
Entering edit mode

I don't install R that way; maybe the r-base-core installation just requires the library but not developer headers. Most people who intend to install packages on top of r-base-core (i.e., just about everyone?) probably want to use r-base-dev.

ADD REPLY
0
Entering edit mode

Sorry, I copied and pasted the wrong example in there.  zlib1g-dev is the dependency for r-base-dev as you say.  

I guess it might still explain why it's missing in this case, although it looks like plenty of other packages with specific system dependencies have been installed previously.

ADD REPLY

Login before adding your answer.

Traffic: 728 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6