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Question: Trouble Installing Bioconductor Basic Packages
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gravatar for tasnif.rahman
3 months ago by
tasnif.rahman0 wrote:

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

ADD COMMENTlink modified 3 months ago by James W. MacDonald48k • written 3 months ago by tasnif.rahman0
1
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald48k wrote:

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 COMMENTlink written 3 months ago by James W. MacDonald48k

That worked. Thank you! 

ADD REPLYlink written 3 months ago by tasnif.rahman0
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