eddelbuettel
commented
2 years ago [ A plea: If you can, please use standard commands as R CMD build ..., R CMD INSTALL ..., R CMD check ... as that is what CRAN uses. It also helps those like myself who work the same rather way rather than via those less-officiel wrapper functions ].
What you show above is mostly a linking / symbol failure. Something may have changed between the NLopt libraries, something may be due to how you are building.
But I just installed nloptr version 2.0.0 as in the repo on the Debian testing system where I run reverse depends (and which hence all I need for your packages which are part of the set).
And it installs (of course), in this case with a build of the included library source. And missSBM installs fine and tests ok as usual. No issues I can reproduce.
```sh
dirk@cloud-devel:~/tmp/prrd$ R_LIBS_USER=~/tmp/lib R CMD check --no-manual --no-vignettes missSBM_1.0.1.tar.gz
* using log directory ‘/home/dirk/tmp/prrd/missSBM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --no-vignettes’
* checking for file ‘missSBM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missSBM’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘missSBM’ can be installed ... [133s/132s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compilation flags used ... WARNING
Compilation used the following non-portable flag(s):
‘-Wno-deprecated-declarations’ ‘-Wno-maybe-uninitialized’ ‘-Wno-nonnull’ ‘-Wno-parentheses’ ‘-Wno-sign-compare’
including flag(s) suppressing warnings
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’ [186s/147s]
[187s/147s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 WARNING
See
‘/home/dirk/tmp/prrd/missSBM.Rcheck/00check.log’
for details.
dirk@cloud-devel:~/tmp/prrd$
```
astamm
To continue the email exchange we had with @astamm ...
With the master version of nloptr (2.0.0), I experience some linking problems during R CMD check on Linux machines in packages missSBM and PLNmodels which I maintain and use nlopt.
With github actions, R CMD check passes for Window and MacOS but not ubuntu : https://github.com/GrossSBM/missSBM/actions/runs/1717379874
Note that I directly call nlopt.h in C++, and @astamm tried a PR to correct this https://github.com/GrossSBM/missSBM/commit/795daec19d1101f2d1e61dd58387aabf863a3cda
but still failing.
Locally, with Ubuntu 20.04 , "R CMD INSTALL --preclean --no-multiarch --with-keep.source missSBM" works (no system nlopt installed) but it fails during the RCMD check process :