Problems with load_all in upcoming R.3.6 release

[epurdom]

Hello,
I am running the upcoming R 3.6 release and trying to make necessary updates to my package for the new release. I am running Mac OS X and have downloaded 3.6 from the mac site (http://R.research.att.com/). I do not have any problem installing packages from source, etc in this new version. But when I try to run load_all, I am getting the following error when trying to compile my C code (which is ominously trying to use a 3.5 location).

Error in dyn.load(dllfile) : 
  unable to load shared object '/Users/epurdom/Documents/Sequencing/SingleCell/packages/clusterExperiment/src/clusterExperiment.so':
  dlopen(/Users/epurdom/Documents/Sequencing/SingleCell/packages/clusterExperiment/src/clusterExperiment.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
  Referenced from: /Users/epurdom/Documents/Sequencing/SingleCell/packages/clusterExperiment/src/clusterExperiment.so
  Reason: image not found

This is particularly problematic, because I can't even run document and update my documentation.

I never had any problem with this package and running load_all until the update, so this might be a problem with the R version as its new and not released. However I do not have any error notices when I run R CMD BUILD or R CMD INSTALL from command line, so I thought I would check here first. If this is a problem with the R version, I'd appreciate any code that would recreate this independent of load_all (i.e. with R CMD command-line) so I can report it.

Thank you,
Elizabeth

> sessionInfo()
R version 3.6.0 alpha (2019-04-09 r76363)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
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] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rmeta_3.0                   survey_3.35-1               survival_2.44-1.1           Matrix_1.2-17               SingleCellExperiment_1.5.2 
 [6] SummarizedExperiment_1.13.0 DelayedArray_0.9.9          BiocParallel_1.17.18        matrixStats_0.54.0          Biobase_2.43.1             
[11] GenomicRanges_1.35.1        GenomeInfoDb_1.19.3         IRanges_2.17.5              S4Vectors_0.21.23           BiocGenerics_0.29.2        
[16] usethis_1.5.0               devtools_2.0.2             

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1        rprojroot_1.3-2         XVector_0.23.2          fs_1.2.7                rstudioapi_0.10         roxygen2_6.1.1         
  [7] remotes_2.0.4           gsl_2.1-6               bit64_0.9-7             AnnotationDbi_1.45.1    RSpectra_0.14-0         mvtnorm_1.0-10         
 [13] xml2_1.2.0              codetools_0.2-16        splines_3.6.0           doParallel_1.0.14       ade4_1.7-13             pkgload_1.0.2          
 [19] locfdr_1.1-8            phylobase_0.8.6         gridBase_0.4-7          annotate_1.61.1         cluster_2.0.8           kernlab_0.9-27         
 [25] stabledist_0.7-1        copula_0.999-19         HDF5Array_1.11.11       httr_1.4.0              BiocManager_1.30.4      compiler_3.6.0         
 [31] backports_1.1.4         assertthat_0.2.1        lazyeval_0.2.2          limma_3.39.15           cli_1.1.0               prettyunits_1.0.2      
 [37] tools_3.6.0             gtable_0.3.0            glue_1.3.1              GenomeInfoDbData_1.2.1  reshape2_1.4.3          dplyr_0.8.0.1          
 [43] Rcpp_1.0.1              softImpute_1.4          zinbwave_1.5.2          NMF_0.21.0              ape_5.3                 nlme_3.1-139           
 [49] iterators_1.0.10        stringr_1.4.0           ps_1.3.0                testthat_2.0.1          rngtools_1.3.1          XML_3.98-1.19          
 [55] edgeR_3.25.4            MASS_7.3-51.4           zlibbioc_1.29.0         scales_1.0.0            hms_0.4.2               rhdf5_2.27.15          
 [61] RColorBrewer_1.1-2      memoise_1.1.0           ggplot2_3.1.1           pkgmaker_0.27           stringi_1.4.3           RSQLite_2.1.1          
 [67] genefilter_1.65.0       desc_1.2.0              clusterExperiment_2.3.4 pcaPP_1.9-73            foreach_1.4.4           pkgbuild_1.0.3         
 [73] bibtex_0.4.2            rlang_0.3.4             pkgconfig_2.0.2         commonmark_1.7          bitops_1.0-6            rncl_0.8.3             
 [79] lattice_0.20-38         purrr_0.3.2             Rhdf5lib_1.5.4          bit_1.1-14              processx_3.3.0          tidyselect_0.2.5       
 [85] plyr_1.8.4              magrittr_1.5            R6_2.4.0                ADGofTest_0.3           DBI_1.0.0               pillar_1.3.1           
 [91] withr_2.1.2             RCurl_1.95-4.12         tibble_2.1.1            pspline_1.0-18          crayon_1.3.4            uuid_0.1-2             
 [97] howmany_0.3-1           progress_1.2.0          RNeXML_2.3.0            locfit_1.5-9.1          blob_1.1.1              callr_3.2.0            
[103] digest_0.6.18           xtable_1.8-3            tidyr_0.8.3             numDeriv_2016.8-1       glmnet_2.0-16           munsell_0.5.0          
[109] registry_0.5-1          sessioninfo_1.1.1      

[jimhester]

You need to first run devtools::clean_dll() if the shared library was built with an earlier version of R.

[epurdom]

Thank you very much, that solved the problem!

[lock]

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/