Trouble Installing Bioconductor Basic Packages
1
0
Entering edit mode
@tasnifrahman-16929
Last seen 6.0 years ago

I am using R version 3.4.4 and Bioconductor version 3.6 with BiocInstaller version 1.28.0 on a Virtual Machine with Windows 7 as the host OS and Linux Mint 19 as the guest OS using VirtualBox version 4.3.12. When I try to install the basic BioConductor Packages with biocLite(), the packages do not install and perform a non-zero exit for each package and dependency that it attempted to install. I had the same issue on a different Windows 10 device, but it seemed to resolve itself. I am new to both Linux and R, and bioinformatics in general so any help is appreciated. 

The code is as follows:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> ?biocLite
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘bit’, ‘digest’, ‘bit64’, ‘memoise’, ‘Rcpp’, ‘S4Vectors’, ‘RSQLite’

trying URL 'https://cloud.r-project.org/src/contrib/bit_1.1-14.tar.gz'
Content type 'application/x-gzip' length 54779 bytes (53 KB)
==================================================
downloaded 53 KB

trying URL 'https://cloud.r-project.org/src/contrib/digest_0.6.15.tar.gz'
Content type 'application/x-gzip' length 122095 bytes (119 KB)
==================================================
downloaded 119 KB

trying URL 'https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz'
Content type 'application/x-gzip' length 125539 bytes (122 KB)
==================================================
downloaded 122 KB

trying URL 'https://cloud.r-project.org/src/contrib/memoise_1.1.0.tar.gz'
Content type 'application/x-gzip' length 11025 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_0.12.18.tar.gz'
Content type 'application/x-gzip' length 3809164 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'
Content type 'application/x-gzip' length 432152 bytes (422 KB)
==================================================
downloaded 422 KB

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.1.1.tar.gz'
Content type 'application/x-gzip' length 2192835 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Biobase_2.38.0.tar.gz'
Content type 'application/x-gzip' length 1656734 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'
Content type 'application/x-gzip' length 485066 bytes (473 KB)
==================================================
downloaded 473 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'
Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c attrutil.c -o attrutil.o
In file included from attrutil.c:1:0:
/usr/share/R/include/R.h:55:11: fatal error: stdlib.h: No such file or directory
 # include <stdlib.h> /* Not used by R itself, but widely assumed in packages */
           ^~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'attrutil.o' failed
make: *** [attrutil.o] Error 1
ERROR: compilation failed for package ‘bit’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/bit’
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c crc32.c -o crc32.o
In file included from crc32.c:23:0:
zutil.h:21:12: fatal error: string.h: No such file or directory
 #  include <string.h>
            ^~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'crc32.o' failed
make: *** [crc32.o] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/digest’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/share/R/include -DNDEBUG -I../inst/include/     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Date.cpp -o Date.o
/bin/bash: g++: command not found
/usr/lib/R/etc/Makeconf:168: recipe for target 'Date.o' failed
make: *** [Date.o] Error 127
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/Rcpp’
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c AEbufs.c -o AEbufs.o
In file included from /usr/share/R/include/Rdefines.h:37:0,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from AEbufs.c:5:
/usr/share/R/include/R_ext/RS.h:34:11: fatal error: string.h: No such file or directory
 # include <string.h>  /* for memcpy, memset */
           ^~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'AEbufs.o' failed
make: *** [AEbufs.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
In file included from Rinit.c:1:0:
/usr/share/R/include/Rinternals.h:39:11: fatal error: stdio.h: No such file or directory
 # include <stdio.h>
           ^~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'Rinit.o' failed
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ‘Biobase’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/Biobase’
ERROR: dependency ‘bit’ is not available for package ‘bit64’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/bit64’
ERROR: dependency ‘digest’ is not available for package ‘memoise’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/memoise’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘bit64’, ‘memoise’, ‘Rcpp’ are not available for package ‘RSQLite’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/RSQLite’
ERROR: dependencies ‘Biobase’, ‘IRanges’, ‘RSQLite’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/rnaseq/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
    ‘/tmp/RtmpxtKGj7/downloaded_packages’
installation path not writeable, unable to update packages: cluster, foreign,
  MASS, Matrix, mgcv, nlme, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘bit’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘digest’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rcpp’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Biobase’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘bit64’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘memoise’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RSQLite’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status

R bioclite installation problem linuxmint virtualbox • 2.0k views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

It looks like you are missing a lot of header files. When you install Linux Mint, it may be simply installing the binaries and not the devel packages (which in general contain the header files). A quick google indicates that you need to install build-essentials, or simply g++.

ADD COMMENT
0
Entering edit mode

That worked. Thank you! 

ADD REPLY

Login before adding your answer.

Traffic: 535 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