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@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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