install error in newest R version

[sanyuanqian]

I installed and run xtail successfully on R v3.4 on my Mac , but when I updated the R version to the newest v3.6 , the installation always failed by github-link or source code with the following error :

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [xtail.so] Error 1
ERROR: compilation failed for package ‘xtail’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/xtail’
  Warning in install.packages :
  installation of package ‘/Users/sunyuanqiang/Desktop/xtail_1.1.5-source.tar’ had non-zero exit status

Any suggestions would be appreaciated !

[xug15]

I get the same erro:

install.packages("/Share/home/tiangeng/miniconda3/package/xtail_1.1.5-source.tar.gz",repo=NULL,type="source")

• installing source package 'xtail' ...
  ** using staged installation
  ** libs
  Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
  argument is of length zero
• removing '/Share/home/tiangeng/miniconda3/lib/R/library/xtail'
  Warning message:
  In install.packages("/Share/home/tiangeng/miniconda3/package/xtail_1.1.5-source.tar.gz", :
  installation of package '/Share/home/tiangeng/miniconda3/package/xtail_1.1.5-source.tar.gz' had non-zero exit status

[xug15]

I fixed this problem using docker.

1. Download docker and install.
2. Get xtail image from docker hub.

docker pull gangxu/xtail:latest

3. Run this image

docker run --name xtail2 -dt gangxu/xtail:latest

4. Get into the xtail and using it.

docker exec -it xtail2 bash
R
library(xtail)

5. exit container

# quit from R
q()
#quite container
exit;

6. Stop container

docker stop xtail2

7. If you need using it agin:

docker start xtail2

[zhengtaoxiao]

I installed and run xtail successfully on R v3.4 on my Mac , but when I updated the R version to the newest v3.6 , the installation always failed by github-link or source code with the following error :

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [xtail.so] Error 1
ERROR: compilation failed for package ‘xtail’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/xtail’
  Warning in install.packages :
  installation of package ‘/Users/sunyuanqiang/Desktop/xtail_1.1.5-source.tar’ had non-zero exit status

Any suggestions would be appreaciated !

It seems you need to install gfortran.

[zhengtaoxiao]

Hi,

Someone got below error when installing the binary version of xtail in a new version R (R 3.6.1):

Error: package or namespace load failed for ‘xtail’:

package ‘xtail’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version

If you meet the same error, please install xtail using the source package by the below command: install_github("xryanglab/xtail")

[cjdecker]

I have previously run xtail successfully on my Mac using an older version of R and Rstudio. I recently updated to R 3.6.1

I got the same error as mentioned above
Error: package or namespace load failed for ‘xtail’:
package ‘xtail’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version

And cannot install xtail successfully in Rstudio. I would appreciate your help in installing xtail. thanks

After downloading the source file, I get the following message

install.packages('xtail_1.1.5-source.tar')
Warning in install.packages :
package ‘xtail_1.1.5-source.tar’ is not available (for R version 3.6.1)

I get the following error when using GitHub after installing and loading devtools

install_github("xryanglab/xtail")
Downloading GitHub repo xryanglab/xtail@master
Skipping 2 packages not available: DESeq2, genefilter
✔ checking for file ‘/private/var/folders/b7/350d_ywj4dxcw2r00333289h0000gn/T/RtmpdHdnXY/remotes2fc686f7484/xryanglab-xtail-a5448a2/DESCRIPTION’ ...
─ preparing ‘xtail’:
✔ 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
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘xtail_1.1.5.tar.gz’

• installing source package ‘xtail’ ...
  ** using staged installation
  ** libs
  clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
  In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
  In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
  In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
  In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:305:
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
  #include_next <math.h>
  ^~~~~~~~
  1 error generated.
  make: *** [RcppExports.o] Error 1
  ERROR: compilation failed for package ‘xtail’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/xtail’
  Error: Failed to install 'xtail' from GitHub:
  (converted from warning) installation of package ‘/var/folders/b7/350d_ywj4dxcw2r00333289h0000gn/T//RtmpdHdnXY/file2fc45675142/xtail_1.1.5.tar.gz’ had non-zero exit status