Enable travis CI to check for package dependencies - r

Actual question
What do I need to do in order to enable travis CI to check my package dependencies?
What I tried
I tried adding the cran argument to .travis.yml file as describe in guide on travis-ci.com.
My .travis.yml file looks like this:
language: r
warnings_are_errors: yes
sudo: required
cran: http://cran.rstudio.com
r_packages:
- covr
after_success:
- Rscript -e 'covr::codecov()'
Yet, I still get the following error:
* checking package dependencies ... ERROR
No repository set, so cyclic dependency check skipped
Session info
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devops_0.1.2
loaded via a namespace (and not attached):
[1] magrittr_1.5 tools_3.2.2 yaml_2.1.13 memoise_0.2.1 stringi_1.0-1
[6] stringr_1.0.0 digest_0.6.8 devtools_1.9.1
Update
I found out that the error was actually cause by listing some package dependencies in Suggests: instead of Imports: section of my DESCRIPTION file (build that passed).
However, I'm still getting a note that the dependency check was skipped as no repository has been set:
* checking package dependencies ... NOTE
No repository set, so cyclic dependency check skipped
Does that mean that a dependency check has not been carried out and, if so, what do I need to change in order to make this happen?

Related

Package 'xxx’ was installed before R 4.0.0: please re-install it (already done fresh install and checked lib paths)

I am having some issue with installing a package in R 4.0.2 from binaries. Here is my attempt:
> install.packages("C:/Users/MNestor/Downloads/libSBML_5.18.0.zip", repos = NULL, type = "win.binary")
Installing package into ‘C:/Users/MNestor/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)
package ‘libSBML’ successfully unpacked and MD5 sums checked
Warning messages:
1: multiple methods tables found for ‘type’
2: multiple methods tables found for ‘type<-’
Next I load library:
> library('libSBML')
Error: package or namespace load failed for ‘libSBML’:
package ‘libSBML’ was installed before R 4.0.0: please re-install it
This error is confusing to me because I am working in R 4.0.2 and have clearly just done a fresh install.
I have tried
deleting the library folder and reinstalling
running remove.packages('libSBML') and reinstalling
For reference here are my library directories:
> .libPaths()
[1] "C:/Users/MNestor/Documents/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.2/library"
The libSMBL folder is located in the first library path, and not the second (as expected).
Here is session info:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] rsbml_2.46.0 BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.2 tools_4.0.2 remotes_2.2.0
[5] stats4_4.0.2 SBMLR_1.84.0 graph_1.66.0
The error message is maybe a bit confusing, but it's saying the package is already compiled for an earlier version of R. (That's what the option "win.binary" means).
R 4.0 and earlier binaries are not compatible because of updated compilers and build tools.
You'll need to install the package from source, which likely means installing R tools (https://cran.r-project.org/bin/windows/Rtools/) or you'll need to use a version that is pre-built for R 4.0 or later.

R error: namespace load failed for ‘ggplot2’

I needed to reinstall R after experiencing the blank non-functional Rstudio. After that I got into big troubles with Rstudio, which now would start but is reacting in a weird way. I installed many times ggplot2 and other packages, after which I am getting a message like:
package ‘ggplot2’ successfully unpacked and MD5 sums checked. The downloaded binary packages are in C:\Users\absolution\AppData\Local\Temp\RtmpIJr2z3\downloaded_packages
But when I upload them I am getting an error message:
Error: package or namespace load failed for ‘ggplot2’ in get(Info[i, 1], envir = env):cannot open file 'C:/Users/absolution/Documents/R/win-library/3.4/Rcpp/R/Rcpp.rdb': No such file or Directory
During this process I also observed twice a pop-up window asking if I would like to create a personal library, I clicked once no and the second time yes. So I dont know whats going on.
Here is what I got in the sessionInfo():
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.4 tools_3.4.4 gtable_0.2.0 grid_3.4.4
I will highly appreciate your help.

R refers to non exisiting files during R CMD check

I want to R CMD check with RStudio my package (for this question I call it pkg). But I get the following error message:
* preparing 'pkg':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Error in find_vignette_product(name, by = "weave", dir = docdir, engine = engine) :
Failed to locate the 'weave' output file (by engine 'utils::Sweave') for vignette with name 'my-vignette'. The following files exist in directory 'C:/Users/name/AppData/Local/Temp/RtmpQLnSjE/Rbuild244434d45c05/pkg/vignettes': 'my-vignette.R', 'my-vignette.Rmd'
Execution halted
Error: Command failed (1)
In addition: Warning message:
`cleanup` is deprecated
Execution halted
Exited with status 1.
One first thing, where something might got wrong is that there is no folder called RtmpQLnSjE in my C:/Users/name/AppData/Local/Temp/ directory. Running my Rmd file by hand, does not generate any errors.
I update RStudio to the latest version 1.1.423 and this is my SessionInfo():
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MCMCglmm_2.25 ape_5.0 coda_0.19-1 lme4_1.1-15 Rcpp_0.12.15 Matrix_1.2-12 hmi_0.9.4
loaded via a namespace (and not attached):
[1] lattice_0.20-35 corpcor_1.6.9 digest_0.6.15 withr_2.1.1 MASS_7.3-48 grid_3.4.3
[7] nlme_3.1-131 cubature_1.3-11 minqa_1.2.4 nloptr_1.0.4 devtools_1.13.4 splines_3.4.3
[13] tools_3.4.3 yaml_2.1.16 parallel_3.4.3 compiler_3.4.3 memoise_1.1.0 tensorA_0.36
Concluding as an answer:
Failed to locate the 'weave' output file
This error can have several root causes and is not always easy to trace down. However, there is a good chance that it is related to code inside the vignette, in particular code navigating directories and such (e.g. setwd() or other functions that may rely on relative paths that could differ between a stand-alone run and the more involved R CMD check)
I recently ran across this when a vignette file had a space in the name (like "My Vignette.Rmd"). It was creating an html file called My-Vignette.html. I think it's the hyphen in the name that was causing issues (based on the answer above along with what I'm seeing.)

R install_github produces error: command failed (5)

I am trying to install the package rpivottable via install_github.
When trying I get the error:
Downloading github repo smartinsightsfromdata/rpivotTable#master
Installing rpivotTable
"C:/R/R-PORT~1/App/R-PORT~1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL \
"C:/Users/..../AppData/Local/Temp/RStudioPortableTemp/RtmpyAFPYw/devtools1df857205157/smartinsightsfromdata-rpivotTable-4c7d219" \
--library="C:/R/R-Portable/App/R-Portable/library" --install-tests
Error: Command failed (5)
Rtools is properly installed, find_rtools returns TRUE.
I am running R on the Rportable version due to limitations on admin policies on the machine. In particular I had to set the PATH from R as I don't have access from Windows, but after installing and reinstalling the PATH contains the two paths to Rtools and gcc bins.
The information on my sessionInfo is here:
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_0.11.1 devtools_1.8.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 digest_0.6.8 git2r_0.10.1 htmltools_0.2.6 httpuv_1.3.2 httr_0.6.1 memoise_0.2.1 mime_0.3 R6_2.0.1
[10] Rcpp_0.11.6 RCurl_1.95-4.6 RJSONIO_1.3-0 rversions_1.0.0 stringr_0.6.2 tools_3.1.3 XML_3.98-1.1 xtable_1.7-4
I don't think the problem is related to the package specifically since before I had the same problem with htmlwidgets if try to install via install_github, and I managed to install it directly from CRAN to solve the problem.
I have checked the code of install_github but I can't find what generates the command failed(5) error message. I have got lost after going down a few levels in the call stack.
Any help would be appreciated.

R Rmetrics packages

I ´ve tried to install some packages from Rmetrics, but it looks I am doing something wrong.
For
https://r-forge.r-project.org/scm/viewvc.php/pkg/fPortfolioBacktest/?logsort=cvs&root=rmetrics&pathrev=4948
I simply used
install.packages("fPortfolioBacktest", repos="http://R-Forge.R-project.org")
but
> install.packages("fPortfolioBacktest", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository http://R-Forge.R-project.org/bin/windows/contrib/2.12
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘fPortfolioBacktest’ is not available
Exactly the same problem is with
https://r-forge.r-project.org/scm/viewvc.php/pkg/Rsocp/?root=rmetrics&pathrev=3690
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Slovak_Slovakia.1250 LC_CTYPE=Slovak_Slovakia.1250 LC_MONETARY=Slovak_Slovakia.1250 LC_NUMERIC=C
[5] LC_TIME=Slovak_Slovakia.1250
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] corpcor_1.5.7 fPortfolio_2130.80 fAssets_2100.78 fCopulae_2110.78 sn_0.4-16
[6] mnormt_1.4-3 robustbase_0.7-0 xlsx_0.3.0 xlsxjars_0.3.0 rJava_0.8-8
[11] ttrTests_1.5 PerformanceAnalytics_1.0.3.2 fTrading_2110.77 fBasics_2110.80 timeSeries_2130.90
[16] timeDate_2130.91 dynlm_0.3-0 car_2.0-8 survival_2.36-3 nnet_7.3-1
[21] MASS_7.3-8 lmtest_0.9-27 tseries_0.10-24 quadprog_1.5-3 quantmod_0.3-15
[26] TTR_0.20-2 xts_0.8-0 zoo_1.6-4 Defaults_1.1-1
loaded via a namespace (and not attached):
[1] grid_2.12.0 lattice_0.19-13 Rglpk_0.3-5 slam_0.1-22 strucchange_1.4-2 tools_2.12.0
Is there a fast way how to install them with all the dependencies? I am using Windows XP
Thanks,
Alex
Thanks for adding the error and your sessionInfo.
As I said in my comment, you're running an old version of R (2.12.0). R-forge only builds binaries for the most recent major revision (2.13.X). You need to either upgrade R or build from source. To build from source on Windows, you will need the Windows toolset.

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