I am a medical doctor (so no computer science background at all) starting to get involved with bioinformatic analyses of big datasets and have used R on my private Windows laptop in the past without any problems.
My department now bought a new powerful Laptop to speed up the analyses and our bioinformatics core facility recommended using a Linux system (which I have never really used before), so now I have this great Ubuntu laptop but I'm getting a little frustrated with just setting up my R environment to start working. I've heard Linux needs some time to get used to and I'm up for the challenge and want to try to understand what I'm doing.
So the problem I have is that I cannot really install certain packages in R. As I said the laptop is brand new and installing R and RStudio was one of the first things I did without changing anything in the basic settings of the laptop. So I was very surprised that I keep getting errors in something as simple as installing those packages. For some reason some packages like
install.packages("tidyverse")
work fine, while others fail. So
install.packages("devtools")
gives me the following output
Installing package into ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘systemfonts’, ‘textshaping’, ‘ragg’, ‘pkgdown’
trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.0.4.tar.gz'
Content type 'application/x-gzip' length 81757 bytes (79 KB)
==================================================
downloaded 79 KB
trying URL 'https://cloud.r-project.org/src/contrib/textshaping_0.3.6.tar.gz'
Content type 'application/x-gzip' length 35722 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.4.tar.gz'
Content type 'application/x-gzip' length 427579 bytes (417 KB)
==================================================
downloaded 417 KB
trying URL 'https://cloud.r-project.org/src/contrib/pkgdown_2.0.7.tar.gz'
Content type 'application/x-gzip' length 871465 bytes (851 KB)
==================================================
downloaded 851 KB
trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
Content type 'application/x-gzip' length 374718 bytes (365 KB)
==================================================
downloaded 365 KB
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the fontconfig freetype2 library. Try installing:
* deb: libfontconfig1-dev (Debian, Ubuntu, etc)
* rpm: fontconfig-devel (Fedora, EPEL)
* csw: fontconfig_dev (Solaris)
* brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.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 MESSAGE] ---------------------------
<stdin>:1:10: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2/systemfonts’
Warning in install.packages :
installation of package ‘systemfonts’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2/textshaping’
Warning in install.packages :
installation of package ‘textshaping’ had non-zero exit status
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2/ragg’
Warning in install.packages :
installation of package ‘ragg’ had non-zero exit status
ERROR: dependency ‘ragg’ is not available for package ‘pkgdown’
* removing ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2/pkgdown’
Warning in install.packages :
installation of package ‘pkgdown’ had non-zero exit status
ERROR: dependency ‘pkgdown’ is not available for package ‘devtools’
* removing ‘/home/jasper/R/x86_64-pc-linux-gnu-library/4.2/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpZcPwU9/downloaded_packages’
After looking online for a couple of days now, I believe that there is a problem with the directories or access to them. When I enter
.libPaths()
in R, it gives me
[1] "/home/jasper/R/x86_64-pc-linux-gnu-library/4.2" "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library" "/usr/lib/R/library"
So I started looking into this and tried to modify R_LIBS_USER part of the Renviron file as described here (How do I change the default library path for R packages) without any success.
When I tried installing another package, I got the message that the path is not writable and I read this might be a permission problem. So I used used chmod -R 777 on the four directories (which as far as I understood gives me all permissions to these folders) that showed up with .libPaths(), but no success either. Repeated reinstallation of R and RStudio did not help either.
Unfortunately my computer science skills quickly find their limit (even working with the terminal to be honest). Since I honestly do not really understand what I am doing and would like to do so while changing files in the root of this new laptop, I am hoping that you can help me out. Quitting and changing back to Windows is not an option for my ego :D .
Here is my sessionInfo():
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 fastmap_1.1.0 cli_3.4.1 htmltools_0.5.4 tools_4.2.2 rstudioapi_0.14 yaml_2.3.6 rmarkdown_2.19
[9] knitr_1.41 xfun_0.35 digest_0.6.31 rlang_1.0.6 evaluate_0.19
I would really appreciate your help!
Thanks a lot,
Jasper
I had this same problem recently when trying to install devtools on a kali linux virtual box.
The way I got around it was to install dev tool directly from the linux command line (terminal) using:
sudo apt-get install r-cran-devtools
This should work on Ubuntu too. Good luck.
I need to use R 3.3.3 for SPSS Modeler 18.1. I am unable to install any packages in this version of R.
I have a version of R 3.5.1 and am successfully using it with RStudio. I need to use R 3.3.3 for SPSS Modeler 18.1. I am unable to install any packages. I tried update.packages(), install.packages with type="source" or "both", tried devtools, but can't install devtools either. I believe there's a binary and source mismatch that needs_compilation, but can't seem to figure out how to fix it. This is happening for every package I can think of that I normally use: dplyr, tidyverse, ggplot2, forecast, etc etc.
install.packages('dplyr')
library('dplyr')
install.packages('pillar')
install.packages('devtools')
> install.packages('dplyr')
also installing the dependency ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
rlang 0.2.0 0.3.1 TRUE
dplyr 0.7.4 0.7.8 TRUE
Binaries will be installed
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/rlang_0.2.0.zip'
Content type 'application/zip' length 754726 bytes (737 KB)
downloaded 737 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/dplyr_0.7.4.zip'
Content type 'application/zip' length 2897358 bytes (2.8 MB)
downloaded 2.8 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘rlang’
package ‘dplyr’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘dplyr’
The downloaded binary packages are in
C:\Users\nipa.onulak\AppData\Local\Temp\Rtmpcbgyh7\downloaded_packages
> library('dplyr')
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘pillar’
Error: package or namespace load failed for ‘dplyr’
> install.packages('pillar')
also installing the dependencies ‘fansi’, ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
fansi 0.2.2 0.4.0 TRUE
rlang 0.2.0 0.3.1 TRUE
pillar 1.2.1 1.3.1 FALSE
Binaries will be installed
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/fansi_0.2.2.zip'
Content type 'application/zip' length 141745 bytes (138 KB)
downloaded 138 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/rlang_0.2.0.zip'
Content type 'application/zip' length 754726 bytes (737 KB)
downloaded 737 KB
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘rlang’
The downloaded binary packages are in
C:\Users\nipa.onulak\AppData\Local\Temp\Rtmpcbgyh7\downloaded_packages
installing the source package ‘pillar’
trying URL 'https://cran.mtu.edu/src/contrib/pillar_1.3.1.tar.gz'
Content type 'application/x-gzip' length 103972 bytes (101 KB)
downloaded 101 KB
ERROR: dependency 'rlang' is not available for package 'pillar'
* removing 'C:/Program Files/R/R-3.3.3/library/pillar'
The downloaded source packages are in
‘C:\Users\nipa.onulak\AppData\Local\Temp\Rtmpcbgyh7\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.3\library" C:\Users\NIPA~1.ONU\AppData\Local\Temp\Rtmpcbgyh7/downloaded_packages/pillar_1.3.1.tar.gz' had status 1
2: In install.packages("pillar") :
installation of package ‘pillar’ had non-zero exit status
> install.packages('devtools')
also installing the dependencies ‘git2r’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’
There are binary versions available but the source versions are later:
binary source needs_compilation
git2r 0.21.0 0.24.0 TRUE
rcmdcheck 1.2.1 1.3.2 FALSE
devtools 1.13.5 2.0.1 FALSE
Binaries will be installed
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘pkgload’
These will not be installed
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/git2r_0.21.0.zip'
Content type 'application/zip' length 3022652 bytes (2.9 MB)
downloaded 2.9 MB
package ‘git2r’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\nipa.onulak\AppData\Local\Temp\Rtmpcbgyh7\downloaded_packages
installing the source packages ‘pkgbuild’, ‘rcmdcheck’, ‘devtools’
trying URL 'https://cran.mtu.edu/src/contrib/pkgbuild_1.0.2.tar.gz'
Content type 'application/x-gzip' length 25264 bytes (24 KB)
downloaded 24 KB
trying URL 'https://cran.mtu.edu/src/contrib/rcmdcheck_1.3.2.tar.gz'
Content type 'application/x-gzip' length 1408582 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cran.mtu.edu/src/contrib/devtools_2.0.1.tar.gz'
Content type 'application/x-gzip' length 388953 bytes (379 KB)
downloaded 379 KB
* installing *source* package 'pkgbuild' ...
** package 'pkgbuild' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'callr', details:
call: loadNamespace(name)
error: there is no package called 'debugme'
ERROR: lazy loading failed for package 'pkgbuild'
* removing 'C:/Program Files/R/R-3.3.3/library/pkgbuild'
ERROR: dependency 'pkgbuild' is not available for package 'rcmdcheck'
* removing 'C:/Program Files/R/R-3.3.3/library/rcmdcheck'
ERROR: dependencies 'pkgbuild', 'pkgload', 'rcmdcheck' are not available for package 'devtools'
* removing 'C:/Program Files/R/R-3.3.3/library/devtools'
The downloaded source packages are in
‘C:\Users\nipa.onulak\AppData\Local\Temp\Rtmpcbgyh7\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.3\library" C:\Users\NIPA~1.ONU\AppData\Local\Temp\Rtmpcbgyh7/downloaded_packages/pkgbuild_1.0.2.tar.gz' had status 1
2: In install.packages("devtools") :
installation of package ‘pkgbuild’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.3\library" C:\Users\NIPA~1.ONU\AppData\Local\Temp\Rtmpcbgyh7/downloaded_packages/rcmdcheck_1.3.2.tar.gz' had status 1
4: In install.packages("devtools") :
installation of package ‘rcmdcheck’ had non-zero exit status
5: running command '"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.3\library" C:\Users\NIPA~1.ONU\AppData\Local\Temp\Rtmpcbgyh7/downloaded_packages/devtools_2.0.1.tar.gz' had status 1
6: In install.packages("devtools") :
installation of package ‘devtools’ had non-zero exit status
#MrFlick, thank you. I was able to navigate and ended up using this site "https://www.r-bloggers.com/using-old-versions-of-r-packages/", and used a link from that post for binaries because I was having a lot of issues with that "https://cran.r-project.org/bin/windows/contrib/", and code example for package devtools: install.packages("https://cran.r-project.org/bin/windows/contrib/3.3/devtools_1.13.5.zip", repos=NULL, type="source"). It all seems to work and load the libraries :). Thank you for the direction!
I recently had some problems installing and using the package "digest" in R-3.4.3, which I used previously in R-3.4.1 with no problem. Below are the messages I received from R.
install.packages("digest", dependencies = TRUE)
trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/3.4/digest_0.6.15.zip'
Content type 'application/zip' length 175238 bytes (171 KB)
downloaded 171 KB
package ‘digest’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\weizha\AppData\Local\Temp\RtmpwhNFrq\downloaded_packages
library(digest)
Error: package or namespace load failed for ‘digest’ in FUN(X[[i]], ...):
no such symbol digest in package E:/R 3.4.3/library/digest/libs/x64/digest.dll
Previously I used install.packages(devtools) in R-3.4.1 which installs "digest" as well, and it all worked fine. Recently work upgraded our operating system to windows 10 (from 7) and installed R-3.4.3 for us, and I couldn't get devtools to work anymore, I figured out it's because digest is not working as has been shown above. I've read everything I can find online, but I have no clue how to fix this.
> .libPaths()
[1] "E:/R-3.4.3/library"
> install.packages("digest", lib="E:/R-3.4.3/library")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.4/digest_0.6.15.zip'
Content type 'application/zip' length 175238 bytes (171 KB)
downloaded 171 KB
package ‘digest’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\weizha\AppData\Local\Temp\RtmpCQY8o1\downloaded_packages
> library(digest)
Error: package or namespace load failed for ‘digest’ in FUN(X[[i]], ...):
no such symbol digest in package E:/R-3.4.3/library/digest/libs/x64/digest.dll
> library("digest", lib.loc="E:/R-3.4.3/library")
Error: package or namespace load failed for ‘digest’ in FUN(X[[i]], ...):
no such symbol digest in package E:/R-3.4.3/library/digest/libs/x64/digest.dll
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
>
> setwd('E:/R-3.4.3')
> install.packages("digest", type="source")
trying URL 'https://cran.csiro.au/src/contrib/digest_0.6.15.tar.gz'
Content type 'application/x-gzip' length 122095 bytes (119 KB)
downloaded 119 KB
* installing *source* package 'digest' ...
** package 'digest' successfully unpacked and MD5 sums checked
** libs
Warning: running command 'make -f "E:/R-34~1.3/etc/x64/Makeconf" -f "E:/R-34~1.3/share/make/winshlib.mk" SHLIB="digest.dll" WIN=64 TCLBIN=64 OBJECTS="aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o"' had status 127
ERROR: compilation failed for package 'digest'
* removing 'E:/R-3.4.3/library/digest'
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\weizha\AppData\Local\Temp\RtmpCQY8o1\downloaded_packages’
Warning messages:
1: running command '"E:/R-3.4.3/bin/x64/R" CMD INSTALL -l "E:\R-3.4.3\library" C:\Users\weizha\AppData\Local\Temp\RtmpCQY8o1/downloaded_packages/digest_0.6.15.tar.gz' had status 1
2: In install.packages("digest", type = "source") :
installation of package ‘digest’ had non-zero exit status
> .libPaths()
[1] "E:/R-3.4.3/library"
> install.packages("digest", type="binary")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.4/digest_0.6.15.zip'
Content type 'application/zip' length 175238 bytes (171 KB)
downloaded 171 KB
package ‘digest’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\weizha\AppData\Local\Temp\Rtmp0UupHr\downloaded_packages
> library(digest)
Error: package or namespace load failed for ‘digest’ in FUN(X[[i]], ...):
no such symbol digest in package E:/R-3.4.3/library/digest/libs/x64/digest.dll
When I manually download the package from CRAN, this is what I received from R
> .libPaths()
[1] "E:/R-3.4.3/library"
> library(digest)
Error: package ‘digest’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
In addition: Warning message:
package ‘digest’ was built under R version 3.5.0
>
I am trying to install the dplyr package from Visual Studio 2017. It has a dependency on pillar.
When I perform an install from the command line, I get:
> install.packages('pillar')
Installing package into ‘C:/Users/Jérôme Verstrynge/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
pillar 1.2.1 1.2.2 FALSE
installing the source package ‘pillar’
trying URL 'http://cran.r-project.org/src/contrib/pillar_1.2.2.tar.gz'
Content type 'application/x-gzip' length 64185 bytes (62 KB)
downloaded 62 KB
* installing *source* package 'pillar' ...
** package 'pillar' successfully unpacked and MD5 sums checked
Warning in file(file, if (append) "a" else "w") :
cannot open file 'C:/Users/Jirtme Verstrynge/Documents/R/win-library/3.3/pillar/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'pillar'
* removing 'C:/Users/Jérôme Verstrynge/Documents/R/win-library/3.3/pillar'
There is a bogus conversion of Jérôme Verstrynge into Jirtme Verstrynge.
How can I work around this?
More information
When I perform Get-WinSystemLocale from Windows 10 PowerShell, I get:
LCID Name DisplayName
---- ---- -----------
2057 en-GB English (United Kingdom)
Sys.getlocale() returns:
[1] "LC_COLLATE=English_United Kingdom.1252;
LC_CTYPE=English_United Kingdom.1252;
LC_MONETARY=English_United Kingdom.1252;
LC_NUMERIC=C;
LC_TIME=English_United Kingdom.1252"
Workaround
I have uninstalled Microsoft R client and reinstalled it from here. The client is now on version 3.4.3.0.
The issue has disappeared for the package pillar, but it is coming back with a package called dendextend while trying to install.packages('seriation').
The error is:
> install.packages('seriation')
Installing package into ‘C:/Users/Jérôme Verstrynge/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependency ‘dendextend’
There is a binary version available but the source version is later:
binary source needs_compilation
dendextend 1.7.0 1.8.0 FALSE
trying URL 'http://cran.r-project.org/bin/windows/contrib/3.4/seriation_1.2-3.zip'
Content type 'application/zip' length 1015954 bytes (992 KB)
downloaded 992 KB
package ‘seriation’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Temp\Rtmpi2lOd8\downloaded_packages
installing the source package ‘dendextend’
trying URL 'http://cran.r-project.org/src/contrib/dendextend_1.8.0.tar.gz'
Content type 'application/x-gzip' length 1758392 bytes (1.7 MB)
downloaded 1.7 MB
* installing *source* package 'dendextend' ...
** package 'dendextend' successfully unpacked and MD5 sums checked
Warning in file(file, if (append) "a" else "w") :
cannot open file 'C:/Users/Jirtme Verstrynge/Documents/R/win-library/3.4/dendextend/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'dendextend'
* removing 'C:/Users/Jérôme Verstrynge/Documents/R/win-library/3.4/dendextend'
In R CMD INSTALL
The downloaded source packages are in
‘C:\Temp\Rtmpi2lOd8\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/MIE74D~1/RCLIEN~1/R_SERVER/bin/x64/R" CMD INSTALL -l "C:\Users\Jérôme Verstrynge\Documents\R\win-library\3.4" C:\Temp\Rtmpi2lOd8/downloaded_packages/dendextend_1.8.0.tar.gz' had status 1
2: In utils::install.packages(...) :
installation of package ‘dendextend’ had non-zero exit status
>
It seems there is an issue in utils::install.packages(...)
Issue solved
Apparently, on top of re-installing Microsoft R Client, the remaining issue was related to missing binary packages not available on CRAN repositories yet.
I doubt this has anything to do with the pillar package, but perhaps with the fact that this package is installed from source (unlike the default which is to install from binary). This problem will eventually resolve itself as the binary version of pillar 1.2.2 becomes available on your CRAN mirror (it's already there on CRAN and on https://cloud.r-project.org/web/packages/pillar/index.html).
What's the value of getOption("repos") on your system?
The mis-encoding of non-ASCII characters in this particular scenario feels like a problem which is best avoided by choosing an ASCII-only and space-free directory name for your home (e.g. C:\Users\jverstry instead of your current setting). To rule out a problem with Visual Studio, you could try installing the package from RGui or from the R terminal, please double-check that the installation path for the package is the same.
I'm running into some bad problems installing and using the DESeq2 package for R.
I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7.
I tried installing DESeq2 using:
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
but it run into a lot of errors (some missing packages for some dependency packages etc...) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files.
Then I tried running few commands and I hope the information from them will help finding the cause of all the errors:
First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth... but it was on Linux)
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
GenomicRanges 1.24.2 1.24.3 TRUE
Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
‘lattice’ ‘mgcv’ ‘survival’
These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]:
n
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’
There is a binary version available but the source version is later:
binary source needs_compilation
Rcpp 0.12.4.5 0.12.7 TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
GenomicRanges 1.24.2 1.24.3 TRUE
Rcpp 0.12.4.5 0.12.7 TRUE
Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
‘lattice’ ‘mgcv’ ‘survival’
These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Then trying to install the DESeq2 package with biocLite (looks like everything is good)
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’
There is a binary version available but the source version is later:
binary source needs_compilation
Rcpp 0.12.4.5 0.12.7 TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
GenomicRanges 1.24.2 1.24.3 TRUE
Rcpp 0.12.4.5 0.12.7 TRUE
Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
‘lattice’ ‘mgcv’ ‘survival’
These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Now loading the DESeq2 library (Errors...):
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
sapply, setdiff, sort, table, tapply, union, unique, unsplit
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘data.table’
Error: package or namespace load failed for ‘DESeq2’
Tried installing the missing package:
> install.packages('data.table', dependencies = TRUE)
also installing the dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’, ‘lme4’, ‘SparseM’, ‘pbkrtest’, ‘quantreg’, ‘mime’, ‘bit’, ‘gtools’, ‘car’, ‘markdown’, ‘yaml’, ‘bdsmatrix’, ‘sandwich’, ‘lmtest’, ‘chron’, ‘testthat’, ‘hexbin’, ‘fastmatch’, ‘xts’, ‘bit64’, ‘gdata’, ‘caret’, ‘knitr’, ‘curl’, ‘zoo’, ‘plm’
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
‘minqa’ ‘nloptr’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘mime’ ‘bit’ ‘gtools’ ‘markdown’
‘yaml’ ‘bdsmatrix’ ‘lmtest’ ‘chron’ ‘testthat’ ‘hexbin’ ‘fastmatch’ ‘xts’ ‘bit64’ ‘caret’
‘curl’ ‘zoo’ ‘data.table’
These will not be installed
installing the source packages ‘pbkrtest’, ‘car’, ‘sandwich’, ‘gdata’, ‘knitr’, ‘plm’
trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
downloaded 161 KB
trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
downloaded 608 KB
trying URL 'https://cran.rstudio.com/src/contrib/sandwich_2.3-4.tar.gz'
Content type 'application/x-gzip' length 466729 bytes (455 KB)
downloaded 455 KB
trying URL 'https://cran.rstudio.com/src/contrib/gdata_2.17.0.tar.gz'
Content type 'application/x-gzip' length 1041264 bytes (1016 KB)
downloaded 1016 KB
trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz'
Content type 'application/x-gzip' length 1017858 bytes (994 KB)
downloaded 994 KB
trying URL 'https://cran.rstudio.com/src/contrib/plm_1.5-12.tar.gz'
Content type 'application/x-gzip' length 1246790 bytes (1.2 MB)
downloaded 1.2 MB
ERROR: dependency 'lme4' is not available for package 'pbkrtest'
* removing 'C:/Program Files/R/R-3.3.1/library/pbkrtest'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/pbkrtest_0.4-6.tar.gz' had status 1
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency 'zoo' is not available for package 'sandwich'
* removing 'C:/Program Files/R/R-3.3.1/library/sandwich'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/sandwich_2.3-4.tar.gz' had status 1
Warning in install.packages :
installation of package ‘sandwich’ had non-zero exit status
ERROR: dependency 'gtools' is not available for package 'gdata'
* removing 'C:/Program Files/R/R-3.3.1/library/gdata'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/gdata_2.17.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘gdata’ had non-zero exit status
ERROR: dependencies 'markdown', 'yaml' are not available for package 'knitr'
* removing 'C:/Program Files/R/R-3.3.1/library/knitr'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/knitr_1.14.tar.gz' had status 1
Warning in install.packages :
installation of package ‘knitr’ had non-zero exit status
ERROR: dependencies 'pbkrtest', 'quantreg' are not available for package 'car'
* removing 'C:/Program Files/R/R-3.3.1/library/car'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/car_2.1-3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependencies 'bdsmatrix', 'zoo', 'sandwich', 'car', 'lmtest' are not available for package 'plm'
* removing 'C:/Program Files/R/R-3.3.1/library/plm'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/plm_1.5-12.tar.gz' had status 1
Warning in install.packages :
installation of package ‘plm’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages’
And sessioninfo:
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Hebrew_Israel.1255 LC_CTYPE=Hebrew_Israel.1255 LC_MONETARY=Hebrew_Israel.1255
[4] LC_NUMERIC=C LC_TIME=Hebrew_Israel.1255
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.2.3 Biobase_2.32.0 GenomicRanges_1.24.2
[4] GenomeInfoDb_1.8.7 IRanges_2.6.1 S4Vectors_0.10.3
[7] BiocGenerics_0.18.0 BiocInstaller_1.22.3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4.5 Formula_1.2-1 cluster_2.0.4 XVector_0.12.1 splines_3.3.1
[6] zlibbioc_1.18.0 munsell_0.4.3 BiocParallel_1.6.6 colorspace_1.2-6 lattice_0.20-33
[11] plyr_1.8.4 tools_3.3.1 nnet_7.3-12 grid_3.3.1 gtable_0.2.0
[16] latticeExtra_0.6-28 survival_2.39-4 Matrix_1.2-7.1 gridExtra_2.2.1 RColorBrewer_1.1-2
[21] ggplot2_2.1.0 acepack_1.3-3.3 rpart_4.1-10 scales_0.4.0 foreign_0.8-66
>
Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop.
I also tried something I found on google:
remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)
but the installation had errors too, I can write them here if needed.
I hope you can see something I can't see and help me solving this issue.
Thanks.
It seems that lots of packages, most importantly data.table and lme4, were not properly compiled.
I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package.
install.packages("pacman")
pacman::p_load(data.table, lme4, lattice, mgcv, survival, zoo, markdown,... <etc>)
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
I just confirmed this works on Windows.
Also note, however, that the error you got has been associated in the past with mirror outages. So if you still get this error try changing your CRAN mirror. install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')
Also make sure that you have RTools.exe installed and working.
biocLite(), install.packages() (and the devtools equivalent?) check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or...? it would be good to hear any speculation you have of how this might have happened).
One solution is to find all available packages
avail = available.packages(repos=BiocInstaller::biocinstallRepos())
then all dependencies
deps0 = tools::package_depenencies("DESeq2", avail)
deps = unique(unlist(deps0, use.names=FALSE))
and unsatisfied dependencies
need = setdiff(deps, rownames(installed.packages()))
I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. And finally, install the problem packages, perhaps also DESeq2.
biocLite(c(need, "DESeq2"))
In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use
BiocInstaller::biocValid()
and would ask more Bioconductor-related questions on the Bioconductor support site
This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer:
What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt.
(I highlighted the important points):
Then I reinstalled R then Rstudio then RTools. I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Finally After 3-4 manual installations of missing packages everything worked.
Sorry for the mediocre English.
I hope I helped somebody.
Try the following
if(! "pacman" %in% installed.packages()) install.packages("pacman")
pacman::p_load(char = packages)
pacman::p_load(DESeq2)
install.packages("DESeq2")
library("DESeq2")