installation of package 'qvalue' had non-zero exit status (
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@66d6b5a2
Last seen 7 days ago
Spain

Hello, I'm having problems with instalation of packages on my univeristy server and get the following errors

(base) [ntilikj@login0 ~]$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("qvalue")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.2 (2015-08-14).
Installing package(s) 'qvalue'
Warning: dependencies 'ggplot2', 'glue' are not available
also installing the dependencies 'stringi', 'stringr', 'reshape2'

trying URL 'http://cran.rstudio.com/src/contrib/stringi_1.7.6.tar.gz'
Content type 'application/x-gzip' length 7600716 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

trying URL 'http://cran.rstudio.com/src/contrib/stringr_1.4.0.tar.gz'
Content type 'application/x-gzip' length 135777 bytes (132 KB)
==================================================
downloaded 132 KB

trying URL 'http://cran.rstudio.com/src/contrib/reshape2_1.4.4.tar.gz'
Content type 'application/x-gzip' length 37307 bytes (36 KB)
==================================================
downloaded 36 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/qvalue_2.2.2.tar.gz'
Content type 'application/x-gzip' length 2757615 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
checking for R_HOME... /home/ntilikj/miniconda3/lib/R
checking for R... /home/ntilikj/miniconda3/lib/R/bin/R
checking for endianness... little
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... yes
checking for cat... /usr/bin/cat
checking for local ICUDT_DIR... icu69/data
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=c++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports the Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /usr/bin/pkg-config
checking with pkg-config for the system ICU4C... 50.1.2
checking for ICU4C >= 55... no
*** ICU4C 50.1.2 has been detected
*** Minimal requirements, i.e., ICU4C >= 55, are not met
*** Trying with 'standard' fallback flags
checking whether an ICU4C-based project can be built... no
*** This version of ICU4C cannot be used.
*** Using the ICU 69 bundle.
checking whether we may compile src/icu69/common/putil.cpp... no
checking whether we may compile src/icu69/common/putil.cpp with -D_XPG6... no
*** The ICU4C bundle cannot be built.
*** Failed to configure package build with the ICU bundle usage.
*** Trying with C++11 compiler disabled.
checking for local ICUDT_DIR... icu55/data
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for elf.h... (cached) yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports the Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... (cached) /usr/bin/pkg-config
checking with pkg-config for the system ICU4C... 50.1.2
checking for ICU4C >= 55... no
*** ICU4C 50.1.2 has been detected
*** Minimal requirements, i.e., ICU4C >= 55, are not met
*** Trying with 'standard' fallback flags
checking whether an ICU4C-based project can be built... no
*** This version of ICU4C cannot be used.
*** Using the ICU 55 bundle.
checking whether we may compile src/icu55/common/umapfile.c... yes
checking whether we may compile src/icu55/common/putil.cpp... yes
checking whether the ICU data library can be downloaded... downloading the ICU data library (icudt)
output path: icu55/data/icudt55l.zip
Error in download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb"): unsupported URL scheme

trying URL 'http://raw.githubusercontent.com/gagolews/stringi/master/src/icu55/data/icudt55l.zip'
Error in download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb"): cannot open URL 'http://raw.githubusercontent.com/gagolews/stringi/master/src/icu55/data/icudt55l.zip'

icudt download failed
Error: Stopping on error
Execution halted
*** *********************************************************************
*** stringi cannot be built.
*** Failed to download the ICU data library (icudt). Stopping now.
*** For build environments that have no internet access,
*** see the INSTALL file for a workaround.
*** *********************************************************************
ERROR: configuration failed for package 'stringi'
* removing '/mnt/lustre/home/ntilikj/miniconda3/lib/R/library/stringi'
ERROR: dependencies 'glue', 'stringi' are not available for package 'stringr'
* removing '/mnt/lustre/home/ntilikj/miniconda3/lib/R/library/stringr'
ERROR: dependency 'stringr' is not available for package 'reshape2'
* removing '/mnt/lustre/home/ntilikj/miniconda3/lib/R/library/reshape2'
ERROR: dependencies 'ggplot2', 'reshape2' are not available for package 'qvalue'
* removing '/mnt/lustre/home/ntilikj/miniconda3/lib/R/library/qvalue'

The downloaded source packages are in
        '/tmp/Rtmp0nwcGF/downloaded_packages'
Old packages: 'KernSmooth', 'boot', 'class', 'codetools', 'lattice', 'nnet',
  'rpart', 'spatial'
Update all/some/none? [a/s/n]: n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'stringi' had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'stringr' had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'reshape2' had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'qvalue' had non-zero exit status
>

I changed the CRAN a few times with chooseCRANmirror() however I always get the same errors (the one above and bellow)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("qvalue")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.2 (2015-08-14).
Installing package(s) 'qvalue'
Warning: unable to access index for repository https://www.stats.bris.ac.uk/R/src/contrib
Warning: dependencies 'ggplot2', 'reshape2' are not available
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/qvalue_2.2.2.tar.gz'
Content type 'application/x-gzip' length 2757615 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

ERROR: dependencies 'ggplot2', 'reshape2' are not available for package 'qvalue'
* removing '/mnt/lustre/home/ntilikj/miniconda3/lib/R/library/qvalue'

The downloaded source packages are in
        '/tmp/Rtmp0nwcGF/downloaded_packages'
Warning: unable to access index for repository https://www.stats.bris.ac.uk/R/src/contrib
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'qvalue' had non-zero exit status
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.6 (Maipo)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.2.2

I know that the R version is old, however I don't have control over the server. When I do work that dont require me using the server I use BiocManager::install () and I hever run into any error.

Thanks for all the help

qvalue • 42 views
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