PREPERROR with Debian Linux, R-devel, GCC ASAN/UBSAN

[paciorek]

We're getting this error when checking our 'nimble' package against R-hub. It looks like something in the underlying build system given the message about bioconductor, which is not something that nimble depends on. Any thoughts?

Installing package dependencies
 373#> /bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
 374#> gcc -std=gnu99 -fsanitize=undefined -fno-omit-frame-pointer
 375#> gcc (Debian 7.3.0-11) 7.3.0
 376#> Copyright (C) 2017 Free Software Foundation, Inc.
 377#> This is free software; see the source for copying conditions. There is NO
 378#> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 379#> g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++98
 380#> g++ (Debian 7.3.0-11) 7.3.0
 381#> Copyright (C) 2017 Free Software Foundation, Inc.
 382#> This is free software; see the source for copying conditions. There is NO
 383#> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 384#> Pandoc:
 385#> /bin/pandoc
 386#> -rwxr-xr-x 1 root root 51855680 Jan 20 16:15 /bin/pandoc
 387#> -rwxr-xr-x 1 root root 45102912 Jan 21 15:33 /bin/pandoc-citeproc
 388#> R Under development (unstable) (2018-03-16 r74418) -- "Unsuffered Consequences"
 389#> Copyright (C) 2018 The R Foundation for Statistical Computing
 390#> Platform: x86_64-pc-linux-gnu (64-bit)
 391#> R is free software and comes with ABSOLUTELY NO WARRANTY.
 392#> You are welcome to redistribute it under certain conditions.
 393#> Type 'license()' or 'licence()' for distribution details.
 394#> Natural language support but running in an English locale
 395#> R is a collaborative project with many contributors.
 396#> Type 'contributors()' for more information and
 397#> 'citation()' on how to cite R or R packages in publications.
 398#> Type 'demo()' for some demos, 'help()' for on-line help, or
 399#> 'help.start()' for an HTML browser interface to help.
 400#> Type 'q()' to quit R.
 401#> Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
 402#> Calls: options ... tryCatch -> tryCatchList -> tryCatchOne ->
 403#> Execution halted
 404#> Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
 405#> Calls: options ... tryCatch -> tryCatchList -> tryCatchOne ->
 406#> Execution halted
 407#> Build step 'Execute shell' marked build as failure
 408#> Pinging https://builder.r-hub.io/build/FAILURE/nimble_0.6-11.tar.gz-2c2f5aa5fa345998c9c89ebb88838e4/2018-06-13T23:55:55Z
 409#> {"status":"ok"}
 410#> Finished: FAILURE

[paciorek]

Meant to mention that on various other platforms, I'm not seeing this problem with our package on R-hub.

[aadler]

I'm getting a 502 Bad gateway error on most test platforms.

[jwood000]

I too am having trouble with this check. I'm suspect that check_with_sanitizers() is some sort of wrapper for this check as the error produced is nearly identical (i.e. 'Error in loadNamespace(name) : there is no package called ‘BiocInstaller’). It should be noted that this error has been occurring starting about 6 weeks ago (the end of April).

[boennecd]

The 502 Bad gateway error seems to be a different issue with http://crandeps.r-pkg.org. However, I get this error now on all platforms I have tested.

The above error seems to come from

Starting Docker container
 352pwd
 353docker run -i --user docker --env-file /tmp/fileJvT0G6 -v /home/ubuntu/workspace/dynamichazard_0.5.2.tar.gz-4c59cd461c7b473c96d8fa460b45599a/dynamichazard_0.5.2.tar.gz:/tmp/dynamichazard_0.5.2.tar.gz --name dynamichazard_0.5.2.tar.gz-4c59cd461c7b473c96d8fa460b45599a-2 sha256:e88d5efff3749f9f4f14a968a90da3494f9bff08446e259bdd22809e4f43ba9e /bin/bash -l
 354#> R Under development (unstable) (2018-06-15 r74904) -- "Unsuffered Consequences"
 355#> Copyright (C) 2018 The R Foundation for Statistical Computing
 356#> Platform: x86_64-pc-linux-gnu (64-bit)
 357#> R is free software and comes with ABSOLUTELY NO WARRANTY.
 358#> You are welcome to redistribute it under certain conditions.
 359#> Type 'license()' or 'licence()' for distribution details.
 360#> Natural language support but running in an English locale
 361#> R is a collaborative project with many contributors.
 362#> Type 'contributors()' for more information and
 363#> 'citation()' on how to cite R or R packages in publications.
 364#> Type 'demo()' for some demos, 'help()' for on-line help, or
 365#> 'help.start()' for an HTML browser interface to help.
 366#> Type 'q()' to quit R.
 367#> > source('https://bioconductor.org/biocLite.R')
 368#> Error in file(filename, "r", encoding = encoding) :
 369#> internet routines cannot be loaded
 370#> Calls: source -> file
 371#> In addition: Warning message:
 372#> In file(filename, "r", encoding = encoding) :
 373#> unable to load shared object '/opt/R-devel/lib64/R/modules//internet.so':
 374#> /lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /opt/R-devel/lib64/R/modules//internet.so)
 375#> Execution halted

The file on https://bioconductor.org/biocLite.R yields an error when sourced . The error message seems very close to ContinuumIO/anaconda-issues#8640.

[boennecd]

The 502 Bad gateway error have been issue before #69.

[jwood000]

Just giving an update here... It looks like all problems have been resolved. I have tested both linux-x86_64-rocker-gcc-san and check_with_sanitizers() with no errors. Additionally, I too was previously receiving the 502 Bad gateway error for many other checks and they all now run as expected with no errors.

[boennecd]

I still get the following on debian-gcc-patched

 354#> R version 3.5.0 Patched (2018-06-15 r74904) -- "Joy in Playing"
 355#> Copyright (C) 2018 The R Foundation for Statistical Computing
 356#> Platform: x86_64-pc-linux-gnu (64-bit)
 357#> R is free software and comes with ABSOLUTELY NO WARRANTY.
 358#> You are welcome to redistribute it under certain conditions.
 359#> Type 'license()' or 'licence()' for distribution details.
 360#> Natural language support but running in an English locale
 361#> R is a collaborative project with many contributors.
 362#> Type 'contributors()' for more information and
 363#> 'citation()' on how to cite R or R packages in publications.
 364#> Type 'demo()' for some demos, 'help()' for on-line help, or
 365#> 'help.start()' for an HTML browser interface to help.
 366#> Type 'q()' to quit R.
 367#> > source('https://bioconductor.org/biocLite.R')
 368#> Error in file(filename, "r", encoding = encoding) :
 369#> internet routines cannot be loaded
 370#> Calls: source -> file
 371#> In addition: Warning message:
 372#> In file(filename, "r", encoding = encoding) :
 373#> unable to load shared object '/opt/R-patched/lib64/R/modules//internet.so':
 374#> /lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /opt/R-patched/lib64/R/modules//internet.so)
 375#> Execution halted

debian-gcc-release seems to work.

[jolars]

Edit: Nevermind; the issue seems to have gone away now.

I just started experiencing this issue, after having r-hub work perfectly just a few days ago. Here is a link to one of the log files

The problem seems to occur here:

Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  : 
  cannot download all files
Calls: cat ... get_cran_deps -> download_json -> download -> <Anonymous>
In addition: Warning message:
In utils::download.file(url, path, method = download_method(), quiet = quiet,  :
  URL 'https://crandeps.r-pkg.org:443/deps/qualpalr,R,randtoolbox,graphics,stats,grDevices,utils,assertthat,Rcpp,RcppParallel,testthat,knitr,maps,rmarkdown,rgl,spelling,covr,Rcpp,RcppParallel,RcppArmadillo': status was '502 Bad Gateway'
Execution halted

This is essentially related to #173 since I also have problems with builds other than this particular one (ASAN/UBSAN)

[gaborcsardi]

Was a server error, should be fine.