Entering edit mode
I am writing a report about the version incompatibility between mzR and Rcpp packages. I have tried updating mzR and upgrading my Bioconductor installation, but they did not work for me.
> devtools::install_github("ftwkoopmans/msdap", upgrade = "never")
Downloading GitHub repo ftwkoopmans/msdap@HEAD
✓ checking for file ‘/private/var/folders/l2/7hwhm6494z72nc5249h_yw2m0000gn/T/RtmpuzATY3/remotesc9d424eff8d/ftwkoopmans-msdap-c7b8ca0/DESCRIPTION’ ...
─ preparing ‘msdap’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘msdap_1.0.1.tar.gz’
* installing *source* package ‘msdap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.8.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so
Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libXrender.1.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libXrender.1.dylib' (no such file)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘msdap’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/msdap’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/l2/7hwhm6494z72nc5249h_yw2m0000gn/T//RtmpuzATY3/filec9d532f662c/msdap_1.0.1.tar.gz’ had non-zero exit status
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 magrittr_2.0.3 usethis_2.1.5 devtools_2.4.3 pkgload_1.2.4
[6] R6_2.5.1 rlang_1.0.2 fastmap_1.1.0 tools_4.1.3 pkgbuild_1.3.1
[11] sessioninfo_1.2.2 cli_3.2.0 withr_2.5.0 ellipsis_0.3.2 remotes_2.4.2
[16] rprojroot_2.0.3 lifecycle_1.0.1 crayon_1.5.1 brio_1.1.3 processx_3.5.3
[21] purrr_0.3.4 callr_3.7.0 fs_1.5.2 ps_1.7.0 curl_4.3.2
[26] testthat_3.1.3 memoise_2.0.1 glue_1.6.2 cachem_1.0.6 compiler_4.1.3
[31] desc_1.4.1 prettyunits_1.1.1
it the future please tag with the package in question. If you do not use the package tag the maintainers will not be auto notified of the question.
Thanks for your reminder! I will do so on my future posts.
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your advice.