Question

"rtracklayer" compilation error

0

Entering edit mode

Biologist ▴ 120

@biologist-9801

Last seen 4.8 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 • 1.7k views

ADD COMMENT • link updated 8.5 years ago by Mike Smith ★ 6.6k • written 8.5 years ago by Biologist ▴ 120

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 • link 8.5 years ago Biologist ▴ 120

score 1 · Answer 1 · 2016-07-05

1

Entering edit mode

Mike Smith ★ 6.6k

@mike-smith

Last seen 3 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 • link 8.5 years ago Mike Smith ★ 6.6k

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 • link 8.5 years ago Martin Morgan 25k

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 • link 8.5 years ago Mike Smith ★ 6.6k

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 • link 8.5 years ago Martin Morgan 25k

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 • link 8.5 years ago Mike Smith ★ 6.6k