To put it simply, my R could not recognize my "libssl.so.1.0.0" installed.
Wondering any one has any suggestion.
For the details:
I was trying to install a R package "devtools",
but had one issue.
install.packages("devtools")
...
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/git2r/libs/git2r.so':
libssl.so.1.0.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/git2r’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/httr’
ERROR: dependencies ‘httr’, ‘git2r’ are not available for package ‘devtools’
* removing ‘/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/devtools’
...
it seemed that "libssl.so.1.0.0" is required.
But when I checked which "openssl" I am using:
$ which openssl
~/.anaconda/bin/openssl
$ ldd ~/.anaconda/bin/openssl
linux-vdso.so.1 => (0x00007fffb0de8000)
libssl.so.1.0.0 => /somewhere/Jun/.anaconda/bin/../lib/libssl.so.1.0.0 (0x00002b0618dca000)
libcrypto.so.1.0.0 => /somewhere/Jun/.anaconda/bin/../lib/libcrypto.so.1.0.0 (0x00002b0619041000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003cae000000)
libc.so.6 => /lib64/libc.so.6 (0x0000003cad800000)
/lib64/ld-linux-x86-64.so.2 (0x0000003cad400000)
So it seems to me that "libssl.so.1.0.0" was there, the problem is that R could not find it.
Any suggestion to solve this?
Update:
Another tempt (following 42-'s kind suggestion in the comments)
Adding dependencies=TRUE for "install.packages" command
install.packages("devtools", dependencies=TRUE)
1: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘openssl’ had non-zero exit status
2: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘git2r’ had non-zero exit status
3: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘httr’ had non-zero exit status
4: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘covr’ had non-zero exit status
5: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘gmailr’ had non-zero exit status
6: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘devtools’ had non-zero exit status
7: In install.packages("devtools", dependencies = TRUE) :
installation of package ‘lintr’ had non-zero exit status
tried to install "git2r" first:
install.packages("git2r",dependencies=TRUE)
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘git2r’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘git2r’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘git2r’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘git2r’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘git2r’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/git2r/libs/git2r.so':
libssl.so.1.0.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/host/somewhere/Jun/Programme/R-3.3.1/lib64/R/library/git2r’
The downloaded source packages are in
‘/tmp/Rtmp55IwjF/downloaded_packages’
Warning message:
In install.packages("git2r", dependencies = TRUE) :
installation of package ‘git2r’ had non-zero exit status
Related
When I try to install ggplot with this code
install.packages("png")
install.packages("RgoogleMaps")
install.packages("ggmap")
library(ggmap)
It returns error
installing to /usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘png’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so':
dlopen(/usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so, 6): Library not loaded: #rpath/libz.1.dylib
Referenced from: /usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/png’
Warning in install.packages :
installation of package ‘png’ had non-zero exit status
ERROR: dependency ‘png’ is not available for package ‘RgoogleMaps’
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/RgoogleMaps’
Warning in install.packages :
installation of package ‘RgoogleMaps’ had non-zero exit status
ERROR: dependencies ‘RgoogleMaps’, ‘png’ are not available for package ‘ggmap’
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/ggmap’
Warning in install.packages :
installation of package ‘ggmap’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/fd/7vyffy191_l3j6fhyqbvsn0r0000gn/T/RtmptKSXHF/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Error in library(ggmap) : there is no package called ‘ggmap’
I am installing all the dependencies that the error says are missing. By adding the install packages before installing the ggmap itself.
I am attempting to install the ivreg package into R (4.0.3) on my Mac (OS Big Sur Intel Version 11.6.8)
I am having what apparently is a fairly common problem installing its dependencies, but I am receiving a slightly different error message. My error message from the command install.packages('ivreg'):
clang: error: -E or -x required when input is from standard input
clang: error: no such file or directory: 'L/usr/local/gfortran/lib'
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix’
Warning in install.packages :
installation of package ‘Matrix’ had non-zero exit status
* installing *source* package ‘MatrixModels’ ...
** package ‘MatrixModels’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘Matrix’ 1.2-18 is being loaded, but >= 1.4.2 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘MatrixModels’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/MatrixModels’
Warning in install.packages :
installation of package ‘MatrixModels’ had non-zero exit status
ERROR: dependency ‘MatrixModels’ is not available for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/quantreg’
Warning in install.packages :
installation of package ‘quantreg’ had non-zero exit status
ERROR: dependency ‘quantreg’ is not available for package ‘car’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
The instrumental bit appears to be the very first two lines, where it's describing something about a gfortran directory. I've tried to install gfortran as well as all of the other dependencies to no avail. When I attempt to do so, I'm told that the packages are unavailable for my version of R.
QUESTION: Is there a way to alleviate this error and install ivreg on my machine?
I am using R version >3.5. I want to install factoextra package on R studio (I use Mac). I tried to install the package directly with dependencies = TRUE, and I also tried to install the dependencies packages one by one. Neither worked.
Here is the error message: (* represents the user on my computer).
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** libs
/Users/*/.R/Makevars:2: *** missing separator. Stop.
ERROR: compilation failed for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/quantreg’
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
/Users/*/.R/Makevars:2: *** missing separator. Stop.
ERROR: compilation failed for package ‘mclust’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mclust’
ERROR: dependencies ‘pbkrtest’, ‘quantreg’ are not available for package ‘car’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ggpubr’
ERROR: dependency ‘ggpubr’ is not available for package ‘factoextra’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/factoextra’
The downloaded source packages are in:
‘/private/var/folders/8v/mfj4t9t54y72cdrz6q84jnjh0000gn/T/RtmpfEwO54/downloaded_packages’
Warning messages:
1: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘quantreg’ had non-zero exit status
2: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘mclust’ had non-zero exit status
3: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘car’ had non-zero exit status
4: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘rstatix’ had non-zero exit status
5: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘ggpubr’ had non-zero exit status
6: In install.packages("factoextra", dependencies = TRUE) :
installation of package ‘factoextra’ had non-zero exit status
any help would be greatly appreciated!!
R packages come in two shapes: as pre-compiled binaries, and as source code. In your case, it seems that the compilation of mclust and quantreg failed, as suggested by the error message
Stop. ERROR: compilation failed for package ‘mclust’
Stop. ERROR: compilation failed for package ‘quantreg’
You could try to force install them from binary by running: install.packages("mclust", type = "binary") and install.packages("quantreg", type = "binary")
I am not a Mac user, but I am trying to help some students to install rattle on their Mac systems. I suggest them to follow zhiyzuo post, which is based on Yihui’s comment. But they get the following errors, although 'brew' is installed on their system:
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in library.dynam(lib, package, package.lib) :
shared object ‘stringi.so’ not found
ERROR: lazy loading failed for package ‘stringr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/stringr’
Warning in install.packages :
installation of package ‘stringr’ had non-zero exit status
ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reshape2’
Warning in install.packages :
installation of package ‘reshape2’ had non-zero exit status
ERROR: dependency ‘reshape2’ is not available for package ‘ggplot2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘stringr’ are not available for package ‘rattle’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rattle’
Warning in install.packages :
installation of package ‘rattle’ had non-zero exit status
I was trying to run a simple code on ggplot2 and got the following error:
source("u1.txt")
Error in library(ggplot2) : there is no package called ‘ggplot2’
Error : package ‘foreign’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘maptools’
* removing ‘/home/shivangi/R/i686-pc-linux-gnu-library/3.0/maptools’
* installing *source* package ‘multcomp’ ...
** package ‘multcomp’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (multcomp)
ERROR: dependencies ‘plyr’, ‘reshape2’, ‘scales’ are not available for package ‘ggplot2’
* removing ‘/home/shivangi/R/i686-pc-linux-gnu-library/3.0/ggplot2’
The downloaded source packages are in
‘/tmp/RtmpOGWrr4/downloaded_packages’
Warning messages:
1: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘plyr’ had non-zero exit status
3: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘testthat’ had non-zero exit status
4: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘reshape2’ had non-zero exit status
5: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘scales’ had non-zero exit status
6: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘Hmisc’ had non-zero exit status
7: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘maptools’ had non-zero exit status
8: In install.packages("ggplot2", dep = TRUE) :
installation of package ‘ggplot2’ had non-zero exit status
I had the same error running ggplot this evening, essentially you need to try to install all the dependencies that failed. For me it was "scales", then "munsell" and then finally (the actual problem) "colorspace" which hadn't be updated since I upgraded to 3.1.1. In your case, it looks like you want to first try installing "foreign" and then try ggplot2 again. Keep loading dependencies that error manually until you find the real problem.
You can specify that the install.packages() call also install all dependent packages:
if(!require(ggplot2)) install.packages('dplyr',dependencies = TRUE)
the above code first checks to see if ggplot2 package is loaded, if not it tries to load the apckage. If it cannot load the package, it then tries to install the package and all of package its dependencies.
With RTools installed, I got this to work:
install.packages("ggplot2", type="source",dependencies = TRUE)
Compiled a few packages...
Make sure your PATH is updated to point to RTools properly, i.e. includes
c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin
at the front.
I am using Rtools32.exe