Pmetrics installation

[Amitkolhe21]

I am trying to install Pmetrics but I am gettinh this error:
Warning message:
In i.p(...) :
installation of package ‘C:/Users/salma/AppData/Local/Temp/RtmpaIkrwB/file1d1c188f4ebf/Pmetrics_2.1.1.tar.gz’ had non-zero exit status
Can you help me?
@mnneely

[Siel]

Hi, Thanks for reaching out Could you please provide us with the whole error message? That way I can try to figure it out. *__________________________* Electronic Engineer PhD in Electronic Engineering and Computer Sciences. Researcher at LAPKB - CHLA/USC

…

On Tue, Dec 10, 2024 at 5:03 PM Amitkolhe21 ***@***.***> wrote: I am trying to install Pmetrics but I am gettinh this error: Warning message: In i.p(...) : installation of package ‘C:/Users/salma/AppData/Local/Temp/RtmpaIkrwB/file1d1c188f4ebf/Pmetrics_2.1.1.tar.gz’ had non-zero exit status Can you help me? @mnneely <https://github.com/mnneely> — Reply to this email directly, view it on GitHub <#247>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHZYHQIM3EDRDDKKJUD4ND2E4NGPAVCNFSM6AAAAABTLUCM7OVHI2DSMVQWIX3LMV43ASLTON2WKOZSG4ZTANRYGM2TSNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Amitkolhe21]

12 errors generated.
make: *** [knn.o] Error 1
ERROR: compilation failed for package ‘Pmetrics’

• removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Pmetrics’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T//RtmpzD2sbg/file36866f77ab63/Pmetrics_2.1.1.tar.gz’ had non-zero exit status

[Amitkolhe21]

I've shared the whole error message, can you help me with that? @Siel

[Siel]

The error says that you don’t have the right building tools in your system to compile one of Pmetrics dependencies. Are you using windows? If so, have you installed rtools? If you are using Linux/Mac make sure you have make and a c++ compiler installed. Please let me know how it goes

…

On Thu, Dec 12, 2024 at 1:32 AM Amitkolhe21 ***@***.***> wrote: I've shared the whole error message, can you help me with that? @Siel <https://github.com/Siel> — Reply to this email directly, view it on GitHub <#247 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHZYHTGWR6YYRCCFOHPRZ32FDRR5AVCNFSM6AAAAABTLUCM7OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZXGU2DSMJUGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Amitkolhe21]

FYI, I'm using Mac,

And I have C language installed on it
PFA, I've attached the screenshot for your reference.

[Siel]

I understand. Now the error you are seeing is related to the building process of one of pmetrics internal dependencies (knn.cpp) I suppose you also have a working cpp compiler. I think your error might be related to #215. It is a problem only affecting newer MacOS systems and the solution is at the end of that thread.

[Siel]

I was expecting the error to be more verbose. As you can see in the issue I linked, the final error is the same but the compilation process gives more information as it fails. By the way, when writing the Makevars file, make sure you point it to the right version of the c++ compiler on your system (I usually use gcc)

[Siel]

If that does not work I could point you to some specific branch of Pmetrics that does not use that dependency anymore.

[Amitkolhe21]

Siel, I followed the steps from the the above solution #215, but still I'm facing issue in installing the Pmetrics,
Following the error I received, for your reference.

library("remotes")
remotes::install_github("LAPKB/Pmetrics")
Downloading GitHub repo LAPKB/Pmetrics@HEAD
Running R CMD build...

• checking for file ‘/private/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T/RtmpEU8h6d/remotes16dd41289e9c/LAPKB-Pmetrics-ee1b703/DESCRIPTION’ ... OK
• preparing ‘Pmetrics’:
• checking DESCRIPTION meta-information ... OK
• cleaning src
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
  Removed empty directory ‘Pmetrics/inst/Examples/Runs’
  Omitted ‘LazyData’ and ‘LazyDataCompression’ from DESCRIPTION
• building ‘Pmetrics_2.1.1.tar.gz’
• installing source package ‘Pmetrics’ ...
  ** using staged installation
  ** libs
  sh: g++-13: command not found
  using SDK: ‘’
  g++-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c knn.cpp -o knn.o
  /bin/sh: g++-13: command not found
  make: *** [knn.o] Error 127
  ERROR: compilation failed for package ‘Pmetrics’
• removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Pmetrics’
  Warning messages:
  1: In missing_devel_warning(pkgdir) :
  Package Pmetrics has compiled code, but no suitable compiler(s) were found. Installation will likely fail.
  Install XCode and make sure it works.
  2: In i.p(...) :
  installation of package ‘/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T//RtmpEU8h6d/file16dd3247e718/Pmetrics_2.1.1.tar.gz’ had non-zero exit status

[mhovd]

@Amitkolhe21, are you still experiencing this issue?
From the latest error message it appears that Pmetrics was unable to find the necessary compiler, e.g. gfortran.
Can you check if you have it installed by providing the output from running which gfortran in your Terminal?

[Amitkolhe21]

@mhovd and @Siel I'm still facing the issue

I've installed gfortran, but still getting the following error

Terminal -

amitkolhe@Amits-MacBook-Air ~ % which gfortran
/usr/local/bin/gfortran
amitkolhe@Amits-MacBook-Air ~ % gfortran
gfortran: fatal error: no input files
compilation terminated.
amitkolhe@Amits-MacBook-Air ~ %

Pmetrics error in R Studio while installing -

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

Natural language support but running in an English locale

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.

library("remotes")
remotes::install_github("LAPKB/Pmetrics")
Downloading GitHub repo LAPKB/Pmetrics@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: rlang (1.1.4 -> 1.1.5 ) [CRAN]
5: bit64 (4.5.2 -> 4.6.0-1) [CRAN]
6: igraph (2.1.2 -> 2.1.3 ) [CRAN]
7: systemfonts (1.1.0 -> 1.2.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
rlang (1.1.4 -> 1.1.5 ) [CRAN]
bit64 (4.5.2 -> 4.6.0-1) [CRAN]
igraph (2.1.2 -> 2.1.3 ) [CRAN]
systemfonts (1.1.0 -> 1.2.0 ) [CRAN]
Installing 4 packages: rlang, bit64, igraph, systemfonts
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/rlang_1.1.4.tgz'
Content type 'application/x-gzip' length 1903020 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/bit64_4.6.0-1.tgz'
Content type 'application/x-gzip' length 575590 bytes (562 KB)

downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/igraph_2.1.2.tgz'
Content type 'application/x-gzip' length 9720193 bytes (9.3 MB)

downloaded 9.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/systemfonts_1.2.0.tgz'
Content type 'application/x-gzip' length 7138024 bytes (6.8 MB)

downloaded 6.8 MB

The downloaded binary packages are in
/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T//Rtmp0MoljX/downloaded_packages
Running R CMD build...

• checking for file ‘/private/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T/Rtmp0MoljX/remotes3ead68d44eed/LAPKB-Pmetrics-ee1b703/DESCRIPTION’ ... OK
• preparing ‘Pmetrics’:
• checking DESCRIPTION meta-information ... OK
• cleaning src
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
  Removed empty directory ‘Pmetrics/inst/Examples/Runs’
  Omitted ‘LazyData’ and ‘LazyDataCompression’ from DESCRIPTION
• building ‘Pmetrics_2.1.1.tar.gz’
• installing source package ‘Pmetrics’ ...
  ** using staged installation
  ** libs
  sh: g++-13: command not found
  using SDK: ‘’
  g++-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c knn.cpp -o knn.o
  /bin/sh: g++-13: command not found
  make: *** [knn.o] Error 127
  ERROR: compilation failed for package ‘Pmetrics’
• removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Pmetrics’
  Warning messages:
  1: In missing_devel_warning(pkgdir) :
  Package Pmetrics has compiled code, but no suitable compiler(s) were found. Installation will likely fail.
  Install XCode and make sure it works.
  2: In i.p(...) :
  installation of package ‘/var/folders/hs/xv0d3xt94pn8ks3hxqgrm17m0000gn/T//Rtmp0MoljX/file3ead7897dd31/Pmetrics_2.1.1.tar.gz’ had non-zero exit status