Interesting. For me, the install bombed with the lattice package (error highlighted below):
WARNING: Rtools is required to build R packages, but is not currently installed.
Downloading GitHub repo IQSS/cem@HEAD
Installing 4 packages: Matching, randomForest, combinat, MatchIt
Installing packages into ‘C:/Users/awells/OneDrive - PopHealthCare/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
Content type 'application/zip' length 1237996 bytes (1.2 MB)
downloaded 1.2 MB
Content type 'application/zip' length 249367 bytes (243 KB)
downloaded 243 KB
Content type 'application/zip' length 42708 bytes (41 KB)
downloaded 41 KB
Content type 'application/zip' length 451985 bytes (441 KB)
downloaded 441 KB
package ‘Matching’ successfully unpacked and MD5 sums checked
package ‘randomForest’ successfully unpacked and MD5 sums checked
package ‘combinat’ successfully unpacked and MD5 sums checked
package ‘MatchIt’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\awells\AppData\Local\Temp\RtmpWOLJ6z\downloaded_packages
WARNING: Rtools is required to build R packages, but is not currently installed.
√ checking for file 'C:\Users\awells\AppData\Local\Temp\RtmpWOLJ6z\remotes5b9c409c5acb\IQSS-cem-de93f7e/DESCRIPTION' (436ms)
- preparing 'cem':
√ checking DESCRIPTION meta-information ...
- 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 'cem_1.1.27.tar.gz'
Installing package into ‘C:/Users/awells/OneDrive - PopHealthCare/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'cem' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package 'lattice' was built under R version 4.0.3
Execution halted
ERROR: lazy loading failed for package 'cem'
* removing 'C:/Users/awells/OneDrive - PopHealthCare/Documents/R/win-library/4.0/cem'
Error: Failed to install 'cem' from GitHub:
(converted from warning) installation of package ‘C:/Users/awells/AppData/Local/Temp/RtmpWOLJ6z/file5b9c26a6ffc/cem_1.1.27.tar.gz’ had non-zero exit status
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Sure thing. I suspect the error is mine. Please see entire transcript below:
>devtools::install_github("IQSS/cem")
Downloading GitHub repo IQSS/cem@HEAD
✓ checking for file ‘/private/var/folders/ls/99kskn5j2rb6s7ghgfydsl50g556b6/T/Rtmp4a1OD6/remotesab2f46a89147/IQSS-cem-de93f7e/DESCRIPTION’ ...
─ preparing ‘cem’:
✓ checking DESCRIPTION meta-information ...
─ 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 ‘cem_1.1.27.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘cem’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error: package or namespace load failed for ‘tcltk’:
.onLoad failed in loadNamespace() for 'tcltk', details:
call: system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE)
error: (converted from warning) running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1
Error: package ‘tcltk’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘cem’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cem’
Error: Failed to install 'cem' from GitHub:
(converted from warning) installation of package ‘/var/folders/ls/99kskn5j2rb6s7ghgfydsl50g556b6/T//Rtmp4a1OD6/fileab2f64d9f08e/cem_1.1.27.tar.gz’ had non-zero exit status
Thank you!
HH
H. E. Hinson, MD MCR FAAN
Associate Director of Clinical Research, Neurocritical Care Program
Associate Professor, Neurology and Emergency Medicine
Oregon Health & Science University
3181 SW Sam Jackson Park Road, CR-127
Portland, OR 97239
Office/Fax: 503 418-1472
Cell: 503 348-8579
Can you please show the full install log as well as the output of session Info () ?
What you posted on stackoverflow and what you write do not match, I can only guess that installation fails but you give us more details we can help.
Stefano
Stefano M. Iacus
Project Officer
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European Commission
Joint Research Centre
Demography, Migration and Governance
Office: 26B 00/40
Via Enrico Fermi 2749
I-21027 Ispra / Italy
Tel +39 0332 78.6088
Fax +39 0332 78.9045
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From: Gary King <thegaryking@gmail.com>
Sent: 04 November 2020 18:14:03
To: Stefano Iacus; IACUS Stefano (JRC-ISPRA)
Subject: Fwd: Re: [cem] CEM back in CRAN? Can you help?
Gary
Gary King - Albert J. Weatherhead III University Professor - Director, IQSS - Harvard University
---------- Forwarded message ---------
From:
Holly Hinson <
hinson@ohsu.edu>
Date: Wed, Nov 4, 2020 at 12:11 PM
Subject: Re: Re: [cem] CEM back in CRAN?
To: King, Gary <
king@harvard.edu>
Hi Gary,
Thank you—I had tried that prior to posting, and was getting an error message that I posted to Stack Overflow:
It seems like the package “tcltk” isn’t behaving as expected?
“Error: package ‘tcltk’ could not be loaded
Execution halted”
Sorry to both you with this! I really appreciate the help!
HH
H. E. Hinson, MD MCR FAAN
Associate Director of Clinical Research, Neurocritical Care Program
Associate Professor, Neurology and Emergency Medicine
Oregon Health & Science University
3181 SW Sam Jackson Park Road, CR-127
Portland, OR 97239
Office/Fax: 503 418-1472
Cell: 503 348-8579
Sorry about that! R changes over time and you have to keep up! We've made the necessary changes and they're just verifying (all are really tiny changes). But if you want to install the new version, you can still do it, straight from our github repository. I put info about how to do this at
GaryKing.org/CEMThanks for your patience!
Gary
Gary King - Albert J. Weatherhead III University Professor - Director, IQSS - Harvard University
Thank you Holly for asking this question. What transpired such that the package was removed? And, to your question, when will the package return?
Thank you.
Aaron
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Hi,
I wondered if anyone knew when CEM might return to CRAN for R?
Thanks!
HH
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