[Bioc-devel] problem installing 'Affycoretools' in linux ubuntu

Thu Mar 2 17:12:20 CET 2017

Hi All,

I am using new version of R studio (Version 1.0.136 – © 2009-2016 RStudio, Inc.) on my linux ubuntu system. I am having problems with installing 'affycoretools' package. below are the warning messages:

> biocLite("affycoretools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘affycoretools’
also installing the dependencies ‘curl’, ‘openssl’, ‘httr’, ‘biomaRt’, ‘AnnotationHub’, ‘genefilter’, ‘RCurl’, ‘GenomeInfoDb’, ‘geneplotter’, ‘biovizBase’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’, ‘Category’, ‘annotate’, ‘AnnotationForge’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘GSEABase’, ‘XML’, ‘DESeq2’, ‘ggbio’, ‘GOstats’, ‘oligoClasses’, ‘ReportingTools’

trying URL 'https://cran.rstudio.com/src/contrib/curl_2.3.tar.gz'
Content type 'application/x-gzip' length 400460 bytes (391 KB)
==================================================
downloaded 391 KB

trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.6.tar.gz'
Content type 'application/x-gzip' length 1239339 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.2.1.tar.gz'
Content type 'application/x-gzip' length 133398 bytes (130 KB)
==================================================
downloaded 130 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/biomaRt_2.30.0.tar.gz'
Content type 'application/x-gzip' length 75971 bytes (74 KB)
==================================================
downloaded 74 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/AnnotationHub_2.6.4.tar.gz'
Content type 'application/x-gzip' length 427930 bytes (417 KB)
==================================================
downloaded 417 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1407436 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'application/x-gzip' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomeInfoDb_1.10.3.tar.gz'
Content type 'application/x-gzip' length 14546069 bytes (13.9 MB)
==================================================
downloaded 13.9 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz'
Content type 'application/x-gzip' length 1426298 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/biovizBase_1.22.0.tar.gz'
Content type 'application/x-gzip' length 2431022 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Rsamtools_1.26.1.tar.gz'
Content type 'application/x-gzip' length 2983757 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomicAlignments_1.10.0.tar.gz'
Content type 'application/x-gzip' length 2121866 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BSgenome_1.42.0.tar.gz'
Content type 'application/x-gzip' length 6057978 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/VariantAnnotation_1.20.2.tar.gz'
Content type 'application/x-gzip' length 1633925 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/rtracklayer_1.34.2.tar.gz'
Content type 'application/x-gzip' length 1377579 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomicFeatures_1.26.3.tar.gz'
Content type 'application/x-gzip' length 830995 bytes (811 KB)
==================================================
downloaded 811 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/OrganismDbi_1.16.0.tar.gz'
Content type 'application/x-gzip' length 194540 bytes (189 KB)
==================================================
downloaded 189 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/ensembldb_1.6.2.tar.gz'
Content type 'application/x-gzip' length 1744935 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Category_2.40.0.tar.gz'
Content type 'application/x-gzip' length 610649 bytes (596 KB)
==================================================
downloaded 596 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.1.tar.gz'
Content type 'application/x-gzip' length 1860820 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/AnnotationForge_1.16.1.tar.gz'
Content type 'application/x-gzip' length 3774373 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomicRanges_1.26.3.tar.gz'
Content type 'application/x-gzip' length 1043065 bytes (1018 KB)
==================================================
downloaded 1018 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/SummarizedExperiment_1.4.0.tar.gz'
Content type 'application/x-gzip' length 978079 bytes (955 KB)
==================================================
downloaded 955 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GSEABase_1.36.0.tar.gz'
Content type 'application/x-gzip' length 236553 bytes (231 KB)
==================================================
downloaded 231 KB

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.5.tar.gz'
Content type 'application/x-gzip' length 1599213 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq2_1.14.1.tar.gz'
Content type 'application/x-gzip' length 1406022 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/ggbio_1.22.3.tar.gz'
Content type 'application/x-gzip' length 1519482 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GOstats_2.40.0.tar.gz'
Content type 'application/x-gzip' length 3027278 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/oligoClasses_1.36.0.tar.gz'
Content type 'application/x-gzip' length 372029 bytes (363 KB)
==================================================
downloaded 363 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/ReportingTools_2.14.0.tar.gz'
Content type 'application/x-gzip' length 2354424 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/affycoretools_1.46.5.tar.gz'
Content type 'application/x-gzip' length 6731444 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl at 1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/openssl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/XML’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/httr’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/biomaRt’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/annotate’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘AnnotationForge’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/AnnotationForge’
ERROR: dependency ‘httr’ is not available for package ‘AnnotationHub’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/AnnotationHub’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/geneplotter’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GenomicRanges’
ERROR: dependencies ‘annotate’, ‘XML’ are not available for package ‘GSEABase’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GSEABase’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’ are not available for package ‘Rsamtools’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/Rsamtools’
ERROR: dependencies ‘GSEABase’, ‘genefilter’, ‘annotate’ are not available for package ‘Category’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/Category’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/SummarizedExperiment’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GenomicAlignments’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’
ERROR: dependencies ‘Category’, ‘annotate’, ‘AnnotationForge’ are not available for package ‘GOstats’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GOstats’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’ are not available for package ‘oligoClasses’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/oligoClasses’
ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/rtracklayer’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/BSgenome’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘RCurl’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/GenomicFeatures’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’, ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/VariantAnnotation’
ERROR: dependencies ‘GenomicFeatures’, ‘GenomicRanges’ are not available for package ‘OrganismDbi’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/OrganismDbi’
ERROR: dependencies ‘GenomicRanges’, ‘GenomicFeatures’, ‘GenomeInfoDb’, ‘rtracklayer’, ‘AnnotationHub’, ‘Rsamtools’ are not available for package ‘ensembldb’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/ensembldb’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/biovizBase’
ERROR: dependencies ‘biovizBase’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’ are not available for package ‘ggbio’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/ggbio’
ERROR: dependencies ‘Category’, ‘GOstats’, ‘annotate’, ‘GSEABase’, ‘XML’, ‘DESeq2’, ‘ggbio’ are not available for package ‘ReportingTools’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/ReportingTools’
ERROR: dependencies ‘GOstats’, ‘oligoClasses’, ‘ReportingTools’ are not available for package ‘affycoretools’
* removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/affycoretools’

The downloaded source packages are in
    ‘/tmp/RtmpPFOwZE/downloaded_packages’
installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival
There were 31 warnings (use warnings() to see them)

I will be greatfull for your help in this.

best,

DA

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