How to force MRAN to get all packages from MRAN (some still coming from CRAN)

[benmarwick]

I have a research compendium in a Docker container, which is linked to a continuous integration service. I have attempted to set the package installation repository to MRAN, and this seems to work for some packages during the install, but not others. Here's a snippet of the log (from https://circleci.com/gh/benmarwick/mjbtramp/161)

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

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.

> options(repos='https://mran.microsoft.com/snapshot/2016-11-08')
> 
> 

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

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.

> devtools::install('.', dep=TRUE, repos = 'https://mran.microsoft.com/snapshot/2016-11-08')
Installing mjbtramp
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/mjbtramp' --library='/usr/local/lib/R/site-library'  \
  --install-tests 

* installing *source* package ‘mjbtramp’ ...
** tests
** help
No man pages found in package  ‘mjbtramp’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mjbtramp)
trying URL 'https://mran.microsoft.com/snapshot/2016-11-08/src/contrib/fitdistrplus_1.0-7.tar.gz'
Content type 'unknown' length 864691 bytes (844 KB)
==================================================
downloaded 844 KB

Installing fitdistrplus
trying URL 'https://cran.rstudio.com/src/contrib/survival_2.40-1.tar.gz'
Content type 'unknown' length 4872012 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

Installing survival
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d6da729bd/survival'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘survival’ ...
** package ‘survival’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agexact.c -o agexact.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agfit4.c -o agfit4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agfit5.c -o agfit5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agmart.c -o agmart.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agmart2.c -o agmart2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agmart3.c -o agmart3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agscore.c -o agscore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agsurv3.c -o agsurv3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agsurv4.c -o agsurv4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c agsurv5.c -o agsurv5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c chinv2.c -o chinv2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c chinv3.c -o chinv3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c cholesky2.c -o cholesky2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c cholesky3.c -o cholesky3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c chsolve2.c -o chsolve2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c chsolve3.c -o chsolve3.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c concordance1.c -o concordance1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c cox_Rcallback.c -o cox_Rcallback.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxcount1.c -o coxcount1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxdetail.c -o coxdetail.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxexact.c -o coxexact.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxfit5.c -o coxfit5.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxfit6.c -o coxfit6.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxmart.c -o coxmart.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxmart2.c -o coxmart2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxph_wtest.c -o coxph_wtest.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxsafe.c -o coxsafe.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxscho.c -o coxscho.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c coxscore.c -o coxscore.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c dmatrix.c -o dmatrix.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c doloop.c -o doloop.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c finegray.c -o finegray.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c pyears1.c -o pyears1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c pyears2.c -o pyears2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c pyears3b.c -o pyears3b.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c pystep.c -o pystep.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survConcordance.c -o survConcordance.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survdiff2.c -o survdiff2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survfit4.c -o survfit4.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survfitci.c -o survfitci.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survpenal.c -o survpenal.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survreg6.c -o survreg6.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survreg7.c -o survreg7.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survregc1.c -o survregc1.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survregc2.c -o survregc2.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c survsplit.c -o survsplit.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic   -c tmerge.c -o tmerge.o
gcc -std=gnu99 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o init.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d4148bf61/fitdistrplus'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘fitdistrplus’ ...
** package ‘fitdistrplus’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fitdistrplus)
trying URL 'https://mran.microsoft.com/snapshot/2016-11-08/src/contrib/ggfortify_0.2.0.tar.gz'
Content type 'unknown' length 3557852 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

Installing ggfortify
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_2.2.0.tar.gz'
Content type 'unknown' length 2210334 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

Installing ggplot2
trying URL 'https://cran.rstudio.com/src/contrib/scales_0.4.1.tar.gz'
Content type 'unknown' length 57703 bytes (56 KB)
==================================================
downloaded 56 KB

Installing scales
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.8.tar.gz'
Content type 'unknown' length 2435852 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

Installing Rcpp
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d19501984/Rcpp'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c Date.cpp -o Date.o
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c Module.cpp -o Module.o
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c api.cpp -o api.o
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c attributes.cpp -o attributes.o
g++ -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic   -c barrier.cpp -o barrier.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rcpp/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1df06aeef/scales'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic   -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic   -c colors.cpp -o colors.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o scales.so RcppExports.o colors.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/scales/libs
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (scales)
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d559dec8/ggplot2'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)
trying URL 'https://cran.rstudio.com/src/contrib/gridExtra_2.2.1.tar.gz'
Content type 'unknown' length 459488 bytes (448 KB)
==================================================
downloaded 448 KB

Installing gridExtra
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d6628973e/gridExtra'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘gridExtra’ ...
** package ‘gridExtra’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gridExtra)
Skipping install of 'scales' from a cran remote, the SHA1 (0.4.1) has not changed since last install.
  Use `force = TRUE` to force installation
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/tmp/Rtmpsfl8Rg/devtools1d1f0b8c2e/ggfortify'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘ggfortify’ ...
** package ‘ggfortify’ successfully unpacked and MD5 sums checked
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggfortify)
trying URL 'https://mran.microsoft.com/snapshot/2016-11-08/src/contrib/ggrepel_0.6.3.tar.gz'
Content type 'unknown' length 1274700 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

We can see that 'fitdistplus' is coming from MRAN, but 'survival' is not, 'ggfortify' comes from MRAN, but 'scales' and 'Rcpp' do not, and so on. Why is this happening?

How can I ensure that EVERY package that my package is dependent on comes from MRAN?

Thanks!

Ben

p.s. I have also posted this question on the Microsoft Developer Network Forum, not sure what you guys prefer...

[andrie]

This has nothing to do with the checkpoint package, but I'll answer with my guess anyway.

You are installing the package from MRAN, but haven't set a CRAN mirror (AFAICT), so some (all?) the dependencies get installed from getOption("repos"). What happens when you explicitly set your CRAN mirror to MRAN?