error using the 'digest' package in R - r

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
>

Related

Problem in the installation of R package rsvg

I'm trying to install r package rsvg without any success. Tried the following two methods:
1. install.packages("rsvg")
install.packages("rsvg")
Installing package into ‘C:/Users/hp/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is
later:
binary source needs_compilation
rsvg 2.3.1 2.3.2 TRUE
installing the source package ‘rsvg’
trying URL 'https://cloud.r-project.org/src/contrib/rsvg_2.3.2.tar.gz'
Content type 'application/x-gzip' length 183798 bytes (179 KB)
downloaded 179 KB
* installing *source* package 'rsvg' ...
** package 'rsvg' successfully unpacked and MD5 sums checked
** using staged installation
** libs
rm -f rsvg.dll rsvg.o
"C:/PROGRA~1/R/R-42~1.1/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.48.8
Error in download.file(sprintf("https://github.com/rwinlib/rsvg/archive/v%s.zip", :
download from 'https://github.com/rwinlib/rsvg/archive/v2.48.8.zip' failed
In addition: Warning message:
In download.file(sprintf("https://github.com/rwinlib/rsvg/archive/v%s.zip", :
URL 'https://codeload.github.com/rwinlib/rsvg/zip/refs/tags/v2.48.8': Timeout of 60 seconds was reached
Execution halted
make: *** [Makevars.win:7: winlibs] Error 1
ERROR: compilation failed for package 'rsvg'
* removing 'C:/Users/hp/AppData/Local/R/win-library/4.2/rsvg'
The downloaded source packages are in
‘C:\Users\hp\AppData\Local\Temp\RtmpmG8xM2\downloaded_packages’
Warning message:
In install.packages("rsvg") :
installation of package ‘rsvg’ had non-zero exit status
2. remotes::install_github("ropensci/rsvg")
library(remotes)
install_github("ropensci/rsvg")
Downloading GitHub repo ropensci/rsvg#HEAD
✔ checking for file 'C:\Users\hp\AppData\Local\Temp\RtmpmG8xM2\remotes5a645f9057ed\ropensci-rsvg-6d9840f/DESCRIPTION'
─ preparing 'rsvg':
checking DESCRIPTION meta-information ...
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building 'rsvg_2.3.2.tar.gz'
Warning:
Warning: file 'rsvg/cleanup' did not have execute permissions: corrected
Warning: file 'rsvg/configure' did not have execute permissions: corrected
Installing package into ‘C:/Users/hp/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package 'rsvg' ...
** using staged installation
** libs
rm -f rsvg.dll rsvg.o
"C:/PROGRA~1/R/R-42~1.1/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.48.8
Error in download.file(sprintf("https://github.com/rwinlib/rsvg/archive/v%s.zip", :
download from 'https://github.com/rwinlib/rsvg/archive/v2.48.8.zip' failed
In addition: Warning messages:
1: In download.file(sprintf("https://github.com/rwinlib/rsvg/archive/v%s.zip", :
downloaded length 35551249 != reported length 43111940
2: In download.file(sprintf("https://github.com/rwinlib/rsvg/archive/v%s.zip", :
URL 'https://codeload.github.com/rwinlib/rsvg/zip/refs/tags/v2.48.8': Timeout of 60 seconds was reached
Execution halted
make: *** [Makevars.win:7: winlibs] Error 1
ERROR: compilation failed for package 'rsvg'
* removing 'C:/Users/hp/AppData/Local/R/win-library/4.2/rsvg'
Warning message:
In i.p(...) :
installation of package ‘C:/Users/hp/AppData/Local/Temp/RtmpmG8xM2/file5a645596780/rsvg_2.3.2.tar.gz’ had non-zero exit status
sessionInfo()
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.4.2
loaded via a namespace (and not attached):
[1] processx_3.8.0 compiler_4.2.1 R6_2.5.1 rprojroot_2.0.3 cli_3.4.1 prettyunits_1.1.1 tools_4.2.1 withr_2.5.0
[9] curl_4.3.3 crayon_1.5.2 callr_3.7.2 ps_1.7.2 pkgbuild_1.3.1
According to this issue, you should first install pkgconfig like this:
install.packages('pkgconfig')
install.packages('rsvg')
library(rsvg)
#> Linking to librsvg 2.48.4
Created on 2022-10-28 with reprex v2.0.2
It looks like you experience some connection issues when installing the required winlib. You could also try to install this first:
remotes::install_github("rwinlib/rsvg")
EDIT: Same suggestion as the comment by #Limey

Why can't I download tidycensus?

When I try download the package tidycensus I get the following error:
> install.packages("tidycensus")
Installing package into ‘C:/Users/krosi/OneDrive/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ellipsis’, ‘lifecycle’, ‘tidyselect’, ‘vctrs’, ‘pillar’, ‘dplyr’, ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
ellipsis 0.3.0 0.3.2 TRUE
lifecycle 0.2.0 1.0.0 FALSE
tidyselect 1.0.0 1.1.1 TRUE
vctrs 0.2.4 0.3.8 TRUE
pillar 1.4.3 1.6.1 FALSE
dplyr 0.8.5 1.0.6 TRUE
rlang 0.4.5 0.4.11 TRUE
tidycensus 0.9.9.2 1.0 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/ellipsis_0.3.0.zip'
Content type 'application/zip' length 44220 bytes (43 KB)
downloaded 43 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/tidyselect_1.0.0.zip'
Content type 'application/zip' length 242507 bytes (236 KB)
downloaded 236 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/vctrs_0.2.4.zip'
Content type 'application/zip' length 1018801 bytes (994 KB)
downloaded 994 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/dplyr_0.8.5.zip'
Content type 'application/zip' length 3256479 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rlang_0.4.5.zip'
Content type 'application/zip' length 1115838 bytes (1.1 MB)
downloaded 1.1 MB
package ‘ellipsis’ successfully unpacked and MD5 sums checked
package ‘tidyselect’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘dplyr’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\krosi\AppData\Local\Temp\RtmpI1FQMN\downloaded_packages
installing the source packages ‘lifecycle’, ‘pillar’, ‘tidycensus’
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.0.tar.gz'
Content type 'application/x-gzip' length 83389 bytes (81 KB)
downloaded 81 KB
trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.6.1.tar.gz'
Content type 'application/x-gzip' length 1111747 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/tidycensus_1.0.tar.gz'
Content type 'application/x-gzip' length 2115609 bytes (2.0 MB)
downloaded 2.0 MB
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.4.5 is being loaded, but >= 0.4.10 is required
ERROR: lazy loading failed for package 'lifecycle'
* removing 'C:/Users/krosi/OneDrive/Documents/R/win-library/3.5/lifecycle'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘lifecycle’ had non-zero exit status
* installing *source* package 'tidycensus' ...
** package 'tidycensus' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'dplyr' 0.8.5 is being loaded, but >= 1.0.0 is required
ERROR: lazy loading failed for package 'tidycensus'
* removing 'C:/Users/krosi/OneDrive/Documents/R/win-library/3.5/tidycensus'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘tidycensus’ had non-zero exit status
ERROR: dependency 'lifecycle' is not available for package 'pillar'
* removing 'C:/Users/krosi/OneDrive/Documents/R/win-library/3.5/pillar'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\krosi\AppData\Local\Temp\RtmpI1FQMN\downloaded_packages’
Here is my sessioninfo:
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.1 assertthat_0.2.1 Matrix_1.2-14 cli_2.0.2 tools_3.5.1 glue_1.4.0 rstudioapi_0.11 yaml_2.2.0 crayon_1.3.4
[10] fansi_0.4.0 grid_3.5.1 lattice_0.20-35
Any ideas?
Restart R and reinstall the package in a clean session: you currently have packages loaded which consequently can’t be reloaded in a newer version.

Having trouble installing certain packages for R

I'm having trouble installing certain packages for R. I have now found this issue with jtools, sjplot, and sjmisc. What is strange about it is that it isn't with all packages, ggplot2 was installed fine as well as the devtools package.
I pasted the output below for trying to install sjplot.
This may just be a coincidence and a may be reading some of it wrong because I'm not very experienced with R, but the thing in common with those that dont work compared to those that don't is that they seem to be .tar.gz instead of .zip.
I see this both in the middle of this log and in the Temp\Rtmps96tec\downloaded_packages folder it spits out at the end. The folder shows previous package downloads and all the ones before these that I am trying now that I am having trouble with have been .zip's
Then in the log it looks like it looks for .zips and its fine, then it looks for .tar.gzs and after those is where the issue that keeps coming up happens, the
"'E:\Program' is not recognized as an internal or external command,
operable program or batch file."
message. After that it doesn't look likr it does anything else successfully besides spit out the file int eh temp folder.
I'd love to be able to get it to work through R, but if there is a way to install manually since I have the .tar.gz downloaded and can just move the files over, but just moving the files that trying to reference library(sjplot) doesn't seem to work. I also tried installing with that tarball instead of the Repository but that didn't work either.
> install.packages("sjPlot")
also installing the dependencies ‘httpuv’, ‘later’, ‘prediction’, ‘shiny’, ‘emmeans’, ‘effects’, ‘ggeffects’, ‘merTools’, ‘modelr’, ‘sjlabelled’, ‘sjmisc’, ‘sjstats’
There are binary versions available but the source versions are later:
binary source needs_compilation
httpuv 1.4.1 1.4.4.1 TRUE
later 0.7.1 0.7.3 TRUE
prediction 0.3.2 0.3.6 FALSE
shiny 1.0.5 1.1.0 FALSE
emmeans 1.1.3 1.2.1 FALSE
effects 4.0-1 4.0-2 FALSE
ggeffects 0.3.2 0.3.4 FALSE
merTools 0.3.0 0.4.1 FALSE
modelr 0.1.1 0.1.2 FALSE
sjlabelled 1.0.8 1.0.11 FALSE
sjmisc 2.7.1 2.7.3 FALSE
sjstats 0.14.2-3 0.15.0 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/httpuv_1.4.1.zip'
Content type 'application/zip' length 1118480 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/later_0.7.1.zip'
Content type 'application/zip' length 605749 bytes (591 KB)
downloaded 591 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/sjPlot_2.4.1.zip'
Content type 'application/zip' length 1054285 bytes (1.0 MB)
downloaded 1.0 MB
package ‘httpuv’ successfully unpacked and MD5 sums checked
package ‘later’ successfully unpacked and MD5 sums checked
package ‘sjPlot’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
installing the source packages ‘prediction’, ‘shiny’, ‘emmeans’, ‘effects’, ‘ggeffects’, ‘merTools’, ‘modelr’, ‘sjlabelled’, ‘sjmisc’, ‘sjstats’
trying URL 'https://cran.rstudio.com/src/contrib/prediction_0.3.6.tar.gz'
Content type 'application/x-gzip' length 34409 bytes (33 KB)
downloaded 33 KB
trying URL 'https://cran.rstudio.com/src/contrib/shiny_1.1.0.tar.gz'
Content type 'application/x-gzip' length 2350156 bytes (2.2 MB)
downloaded 2.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/emmeans_1.2.1.tar.gz'
Content type 'application/x-gzip' length 571200 bytes (557 KB)
downloaded 557 KB
trying URL 'https://cran.rstudio.com/src/contrib/effects_4.0-2.tar.gz'
Content type 'application/x-gzip' length 2021373 bytes (1.9 MB)
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/src/contrib/ggeffects_0.3.4.tar.gz'
Content type 'application/x-gzip' length 239215 bytes (233 KB)
downloaded 233 KB
trying URL 'https://cran.rstudio.com/src/contrib/merTools_0.4.1.tar.gz'
Content type 'application/x-gzip' length 476671 bytes (465 KB)
downloaded 465 KB
trying URL 'https://cran.rstudio.com/src/contrib/modelr_0.1.2.tar.gz'
Content type 'application/x-gzip' length 118432 bytes (115 KB)
downloaded 115 KB
trying URL 'https://cran.rstudio.com/src/contrib/sjlabelled_1.0.11.tar.gz'
Content type 'application/x-gzip' length 131062 bytes (127 KB)
downloaded 127 KB
trying URL 'https://cran.rstudio.com/src/contrib/sjmisc_2.7.3.tar.gz'
Content type 'application/x-gzip' length 187915 bytes (183 KB)
downloaded 183 KB
trying URL 'https://cran.rstudio.com/src/contrib/sjstats_0.15.0.tar.gz'
Content type 'application/x-gzip' length 339472 bytes (331 KB)
downloaded 331 KB
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/prediction_0.3.6.tar.gz' had status 1
Warning in install.packages :
installation of package ‘prediction’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/shiny_1.1.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/emmeans_1.2.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘emmeans’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/effects_4.0-2.tar.gz' had status 1
Warning in install.packages :
installation of package ‘effects’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/modelr_0.1.2.tar.gz' had status 1
Warning in install.packages :
installation of package ‘modelr’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/merTools_0.4.1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘merTools’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/sjlabelled_1.0.11.tar.gz' had status 1
Warning in install.packages :
installation of package ‘sjlabelled’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/sjmisc_2.7.3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘sjmisc’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/sjstats_0.15.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘sjstats’ had non-zero exit status
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec/downloaded_packages/ggeffects_0.3.4.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ggeffects’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages’
Thanks for any help!
Edit: I tried installing from the tools menu from the files in temp but got a similar error:
> install.packages("C:/Users/Coldzero/AppData/Local/Temp/Rtmps96tec/downloaded_packages/sjstats_0.15.0.tar.gz", repos = NULL, type = "source")
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "E:\Program Files\R\R-3.3.3\library" "C:/Users/Coldzero/AppData/Local/Temp/Rtmps96tec/downloaded_packages/sjstats_0.15.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/Coldzero/AppData/Local/Temp/Rtmps96tec/downloaded_packages/sjstats_0.15.0.tar.gz’ had non-zero exit status
I also tried using devtools to install straight from github:
install_github("strengejacke/sjPlot")
> install_github("strengejacke/sjPlot")
Downloading GitHub repo strengejacke/sjPlot#master
from URL https://api.github.com/repos/strengejacke/sjPlot/zipball/master
Installing sjPlot
Installing 1 package: arm
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/arm_1.10-1.zip'
Content type 'application/zip' length 219529 bytes (214 KB)
downloaded 214 KB
package ‘arm’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Installing 1 package: effects
There is a binary version available (and will be installed) but the source version is later:
binary source
effects 4.0-1 4.0-2
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/effects_4.0-1.zip'
Content type 'application/zip' length 1508494 bytes (1.4 MB)
downloaded 1.4 MB
package ‘effects’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Installing 1 package: ggeffects
There is a binary version available (and will be installed) but the source version is later:
binary source
ggeffects 0.3.2 0.3.4
also installing the dependencies ‘emmeans’, ‘modelr’, ‘prediction’, ‘sjlabelled’, ‘sjmisc’, ‘sjstats’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/emmeans_1.1.3.zip'
Content type 'application/zip' length 1052492 bytes (1.0 MB)
downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/modelr_0.1.1.zip'
Content type 'application/zip' length 135311 bytes (132 KB)
downloaded 132 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/prediction_0.3.2.zip'
Content type 'application/zip' length 140872 bytes (137 KB)
downloaded 137 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/sjlabelled_1.0.8.zip'
Content type 'application/zip' length 205033 bytes (200 KB)
downloaded 200 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/sjmisc_2.7.1.zip'
Content type 'application/zip' length 311847 bytes (304 KB)
downloaded 304 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/sjstats_0.14.2-3.zip'
Content type 'application/zip' length 378915 bytes (370 KB)
downloaded 370 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/ggeffects_0.3.2.zip'
Content type 'application/zip' length 264629 bytes (258 KB)
downloaded 258 KB
package ‘emmeans’ successfully unpacked and MD5 sums checked
package ‘modelr’ successfully unpacked and MD5 sums checked
package ‘prediction’ successfully unpacked and MD5 sums checked
package ‘sjlabelled’ successfully unpacked and MD5 sums checked
package ‘sjmisc’ successfully unpacked and MD5 sums checked
package ‘sjstats’ successfully unpacked and MD5 sums checked
package ‘ggeffects’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Installing 1 package: knitr
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/knitr_1.20.zip'
Content type 'application/zip' length 892099 bytes (871 KB)
downloaded 871 KB
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Installing 1 package: lme4
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/lme4_1.1-17.zip'
Content type 'application/zip' length 5220055 bytes (5.0 MB)
downloaded 5.0 MB
package ‘lme4’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Skipping install of 'modelr' from a cran remote, the SHA1 (0.1.1) has not changed since last install.
Use `force = TRUE` to force installation
Installing 1 package: psych
There is a binary version available (and will be installed) but the source version is later:
binary source
psych 1.8.3.3 1.8.4
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/psych_1.8.3.3.zip'
Content type 'application/zip' length 5388180 bytes (5.1 MB)
downloaded 5.1 MB
package ‘psych’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Installing 1 package: scales
also installing the dependency ‘viridisLite’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/viridisLite_0.3.0.zip'
Content type 'application/zip' length 56811 bytes (55 KB)
downloaded 55 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/scales_0.5.0.zip'
Content type 'application/zip' length 692819 bytes (676 KB)
downloaded 676 KB
package ‘viridisLite’ successfully unpacked and MD5 sums checked
package ‘scales’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Coldzero\AppData\Local\Temp\Rtmps96tec\downloaded_packages
Skipping install of 'sjlabelled' from a cran remote, the SHA1 (1.0.8) has not changed since last install.
Use `force = TRUE` to force installation
Skipping install of 'sjmisc' from a cran remote, the SHA1 (2.7.1) has not changed since last install.
Use `force = TRUE` to force installation
Skipping install of 'sjstats' from a cran remote, the SHA1 (0.14.2-3) has not changed since last install.
Use `force = TRUE` to force installation
"E:/Program Files/R/R-3.3.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
"C:/Users/Coldzero/AppData/Local/Temp/Rtmps96tec/devtools42282da83eaa/strengejacke-sjPlot-87179d5" --library="E:/Program Files/R/R-3.3.3/library" \
--install-tests
'E:\Program' is not recognized as an internal or external command,
operable program or batch file.
Installation failed: Command failed (1)
Edit2:
I looked at the topic at github.com/r-lib/devtools/issues/1514. It was disabled for my E: drive but I enabled it, rebooted RStudio and I'm still having an issue for all three methods of installation. Still seems to be .tar.gz because I had a short moment of excitement when it worked for one of the dependencies in the folder that was a zip that I tried first.
Edit3:
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.13.5
loaded via a namespace (and not attached):
[1] httr_1.2.1 tidyr_0.8.0 splines_3.3.3 carData_3.0-1 modelr_0.1.1 assertthat_0.2.0 stats4_3.3.3 coin_1.2-2
[9] yaml_2.1.14 pillar_1.2.2 lattice_0.20-34 glue_1.2.0 digest_0.6.12 glmmTMB_0.2.0 snakecase_0.9.1 minqa_1.2.4
[17] colorspace_1.3-2 sandwich_2.3-4 Matrix_1.2-8 survey_3.33-2 plyr_1.8.4 psych_1.8.3.3 pkgconfig_2.0.1 broom_0.4.4
[25] haven_1.1.1 xtable_1.8-2 purrr_0.2.4 mvtnorm_1.0-7 scales_0.5.0 stringdist_0.9.4.7 lme4_1.1-17 emmeans_1.1.3
[33] git2r_0.21.0 arm_1.10-1 tibble_1.4.2 effects_4.0-1 bayesplot_1.5.0 ggplot2_2.2.1 sjlabelled_1.0.8 TH.data_1.0-8
[41] withr_2.1.2 TMB_1.7.13 nnet_7.3-12 lazyeval_0.2.0 cli_1.0.0 mnormt_1.5-5 survival_2.40-1 magrittr_1.5
[49] crayon_1.3.4 memoise_1.1.0 estimability_1.3 nlme_3.1-131 MASS_7.3-47 forcats_0.3.0 foreign_0.8-67 tools_3.3.3
[57] data.table_1.10.4 multcomp_1.4-8 stringr_1.2.0 munsell_0.4.3 prediction_0.3.2 bindrcpp_0.2.2 ggeffects_0.3.2 rlang_0.2.0
[65] grid_3.3.3 nloptr_1.0.4 ggridges_0.5.0 rstudioapi_0.7 gtable_0.2.0 codetools_0.2-15 abind_1.4-5 sjstats_0.14.2-3
[73] curl_2.4 reshape2_1.4.2 sjmisc_2.7.1 R6_2.2.0 zoo_1.8-0 pwr_1.2-2 knitr_1.20 dplyr_0.7.4
[81] bindr_0.1.1 modeltools_0.2-21 stringi_1.1.5 parallel_3.3.3 Rcpp_0.12.16 lmtest_0.9-35 tidyselect_0.2.4 coda_0.19-1
Seems like that's an old version of R was trying to find the version earlier but only found the rstudio version then forgot I was looking for it...

Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems

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")

Why do I get this error installing rmarkdown

I try to use rmarkdown and I've got many troubles so far. The first one is when the Rstudio as if it should install new versions of packages. It can not go over it. I tried to install one by one all the required packages but than I got this error
trying URL 'https://cran.rstudio.com/bin/windows/contrib/2.15/knitr_1.5.zip'
Content type 'application/zip' length 910172 bytes (888 Kb)
opened URL
downloaded 888 Kb
package ‘evaluate’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘formatR’ successfully unpacked and MD5 sums checked
package ‘highr’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\Rtmpcz1Ywk\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
I installed packages one by one and I can load them but it does not work as a whole i.r. file -> new -> rmarkdown
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
[5] LC_TIME=Swedish_Sweden.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rmarkdown_0.9.6 knitr_1.12.3
loaded via a namespace (and not attached):
[1] digest_0.6.9 htmltools_0.3.5 Rcpp_0.12.4 tools_3.1.2
I spotted recently that I got this kind of message when starting Rstudio
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.
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
>
I did as #DAV recommended. Tried to install other version. No success
> url <- "https://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.0.tar.gz"
> install.packages(url, repos=NULL, type="source")
Installing package into ‘\\xxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.0.tar.gz'
Content type 'application/x-gzip' length 451348 bytes (440 Kb)
opened URL
downloaded 440 Kb
* installing *source* package 'knitr' ...
** package 'knitr' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Warning in file(con, "r") :
file("") only supports open = "w+" and open = "w+b": using the former
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
there is no package called 'knitr'
Error: loading failed
Execution halted
ERROR: loading failed
* removing '\\xxxxxx/users/Eke/mali/Documents/R/win-library/3.1/knitr'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/i386/R" CMD INSTALL -l "\\xxxxx\users\Eke\mali\Documents\R\win-library\3.1" "C:/Users/mali/AppData/Local/Temp/RtmpoN1qrM/downloaded_packages/knitr_1.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/mali/AppData/Local/Temp/RtmpoN1qrM/downloaded_packages/knitr_1.0.tar.gz’ had non-zero exit status
It drives me crazy. I uninstalled "knitr" and tried to install again. ERROR
> install.packages("knitr", dependencies = F)
Installing package into ‘\\xxxx.se/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/knitr_1.12.3.zip'
Content type 'application/zip' length 812186 bytes (793 Kb)
opened URL
downloaded 793 Kb
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpaChLQ5\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
And it happened when I wanted to install shiny
> install.packages("shiny", dependencies = F)
Installing package into ‘\\xxxxx.xxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/shiny_0.13.2.zip'
Content type 'application/zip' length 2257481 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb
package ‘shiny’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpC0nOFC\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
You can tell RStudio the location of your library through the .libPaths()
command and then manually selecting knitr and the other packages necessary to use the "rmarkdown" documents in RStudio through the Packages window in your screen.
getwd()
# "C:/Users/s146753/Dropbox/Chapter 2"
.libPaths()
# "\\\\home2.bio.ed.ac.uk/s146753/R/win-library/3.3" "C:/Program Files/R/R-3.3.2/library"
.libPaths("C:/Program Files/R/R-3.3.2/library")
.libPaths()
# "C:/Program Files/R/R-3.3.2/library"

Resources