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Error in Hmisc installation for R 3.4.3 #82
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I'm not sure of a fix yet but I can see that |
Hello -- Hmisc fails to compile for me as well. I manually installed backports as shown above and still had the failure. backports install was done with Hmisc install was attempted with output was:
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Be sure to work with the package maintainer for |
Failure to install in RStudio Version 1.1.412 on Intel Mac OS X 10_11_6
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I'll look for a Mac user to give us the general solution. This problem is not occuring on linux or windows to my knowledge. |
No. I have this problems in Windows too.
…On Jan 23, 2018 17:45, "Frank Harrell" ***@***.***> wrote:
I'll look for a Mac user to give us the general solution. This problem is
not occuring on linux or windows to my knowledge.
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I believe @adeslatt and @stuzog (Mac users) are encountering a different installation problem than @StatsQuo. I am able to install Hmisc 4.1-1 source on macos sierra (10.12.6). My best guess is that the Mac users should try re-installing |
@StatsQuo Were you able to manually install |
Since updating RStudio to 1.1.414 Hmisc 4.1-1 now installs from CRAN. And yes, the file /Library/Frameworks/R.framework/Resources/etc/Makeconf does exist on the system, including the flag FLIBS: FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm Thanks @couthcommander for your response. Whatever bug seems to have been resolved in the RStudio update. |
Thanks @couthcommander, I did as you recommended. I used Homebrew to reinstall gcc
I checked then within R
seemingly succeeded then failed with this error I did as one might guess succeeded. I am able now to compile Hmisc |
@adeslatt I'm not familiar with Bioconductor at all. If you start a new R session without bioconductor loaded, I assume you can load Hmisc successfully? |
@couthcommander -- you are correct! As an aside, in the world of biological sequence data and the need to analyze, bioconductor is a means by which to get that job done and to scale efficiently. Biological data is diverse and not always consistent, bioconductor is an organized structure of creating systematic tools and enabling the researcher to efficiently get all annotations associated with known or orthologous genomes....! this is a website that can give you an introduction if you are interested. https://www.bioconductor.org/help/course-materials/2016/BiocIntro-May/ Thank you for your help! |
Does anyone have suggestions for how the other packages can be permanently fixed to avoid these problems? I haven't seen anything that would suggest |
I am a relatively new R user and am attempting to use rcorr (in Hmisc package for correlation matrix with p-values). I'm using RStudio Version 1.1.423 on Windows 10. Unfortunately, I am having problems installing Hmisc:
@couthcommander: I tried to manually install backports, but received the following error:
Any help would be appreciated, thanks. [UPDATE] A bit more searching led me to a solution: Manually install an older version of backports. Hmisc compiled just fine for me after that. |
Manually download .zip file from https://cran.r-project.org/web/packages/backports/index.html Now, type in console:
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Tried solutions above and did not work for me. This manually install helped me out. tidyverts/fable#107 |
This may have been resolved in some of the R updates since this was originally posted. |
./inst/include/Eigen/src/Core/CoreEvaluators.h:989:54: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
The downloaded source packages are in it also happens in Linux |
@ysh-rawat-11 Your underlying problem are the packages "RcppEigen" and "jpeg". Install the development files for liblapack, libblas, and libjpeg. If you were on a Debian based system you could run Once those are installed, try |
I am getting the following error (in bold text) when using:
Installing package into ‘C:/Users/user/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://repo.bppt.go.id/cran/bin/windows/contrib/3.4/Hmisc_4.0-3.zip'
Content type 'application/zip' length 1792302 bytes (1.7 MB)
downloaded 1.7 MB
package ‘Hmisc’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\RtmpWGOFzV\downloaded_packages
Thanks in advance!!
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