minfi and lumi not available for version 3.3.2
2
1
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@jessiejohnson-12434
Last seen 5.6 years ago

I'm trying to download the minfi and lumi packages, but get warnings with biocLite.

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

> biocLite("lumi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘lumi’
also installing the dependencies ‘curl’, ‘httr’, ‘openssl’, ‘TxDb.Hsapiens.UCSC.                                    hg19.knownGene’, ‘bumphunter’, ‘GEOquery’, ‘base64’, ‘Rsamtools’, ‘GenomicAlignm                                    ents’, ‘affyio’, ‘FDb.InfiniumMethylation.hg19’, ‘minfi’, ‘GenomeInfoDb’, ‘Summa                                    rizedExperiment’, ‘genefilter’, ‘illuminaio’, ‘RCurl’, ‘XVector’, ‘Biostrings’,                                     ‘rtracklayer’, ‘biomaRt’, ‘XML’, ‘affy’, ‘methylumi’, ‘GenomicFeatures’, ‘Genomi                                    cRanges’, ‘annotate’

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/lumi_2.26.4.t                                    ar.gz'
Content type 'unknown' length 9301111 bytes (8.9 MB)
==================================================
downloaded 8.9 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 ‘/work/04595/jnicodem/hikari/apps/R/3.3.2/lib64/R/library/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’

** libs
mpicc -std=gnu99 -I/work/04595/jnicodem/hikari/apps/R/3.3.2/lib64/R/include -DND                                    EBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE                                    _STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHA                                    VE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STR                                    INGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBPTHRE                                    AD=1 -DUSE_PTHREADS=1 -fPIC -qopenmp -mkl=parallel -O3 -xHost  -L/opt/apps/intel                                    /16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_rt -I                                    /work/04595/jnicodem/hikari/apps/xz/5.2.3/include   -g -O2   -fpic -fPIC -qopenm                                    p -mkl=parallel -O3 -xHost   -fPIC -qopenmp -mkl=parallel -O3 -xHost  -L/opt/app                                    s/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmk                                    l_rt -I/work/04595/jnicodem/hikari/apps/xz/5.2.3/include  -c fread_functions.c -                                    o fread_functions.o
In file included from fread_functions.c(10):
fread_functions.h(12): catastrophic error: cannot open source file "zlib.h"
  #include <zlib.h>
                   ^


The downloaded source packages are in
        ‘/tmp/RtmprJ5txV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 28 warnings (use warnings() to see them)

 

minfi lumi • 1.3k views
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I tried bioclite, and received warnings that many dependencies were not available.  

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Add the output of your biocLite() attempt to your QUESTION. Include the output of sessionInfo(). Here's mine...

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("lumi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 Patched (2017-02-14
  r72175).
Installing package(s) 'lumi'
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/lumi_2.26.4.tar.gz'
Content type 'application/x-gzip' length 9301111 bytes (8.9 MB)
==================================================
downloaded 8.9 MB

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
* DONE (lumi)

The downloaded source packages are in
    '/tmp/RtmpiYEgwI/downloaded_packages'
> sessionInfo()
R version 3.3.2 Patched (2017-02-14 r72175)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2
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Thank you I what you suggested.

Best, 

Jessie

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Entering edit mode
@kasper-daniel-hansen-2979
Last seen 7 days ago
United States
Use biocLite() Best, Kasper (Sent from my phone.)
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@martin-morgan-1513
Last seen 17 days ago
United States

Your sessionInfo() tells us that you are on a Linux-based system. The biocLite() output starts by telling us that you are running a current version of R and an appropriate version of BiocInstaller.

Usually it is best to start with the first error that occurs. In this case it is from trying to install the dependency 'curl', and the attempt at installation, concluding with the error, is

* 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

The solution is to install the libcurl system dependency, using your operating system package manager. Once the dependency is installed, you should start a new R session and try again; note that you will (from your output above) run into a second system dependency requiring installation, so you can short circuit things a bit by installing openssl-devel. There may be additional errors from missing system dependencies, and the errors may be less helpful than these two.

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Thank you!  I will try to work my way through this now that I understand this a bit better.

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