Installation error to do with 'lpsymphony' and 'openmp'

[swvanderlaan]

Hi,

I am trying to install this on my MacOS Mojave 10.14.3. However, I get this error - see below.

Do you have any suggestions as to how to fix this?

Thanks!

Sander

r

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin18.2.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ipak <- function(pkg, repository = c("CRAN", "Bioconductor", "github")) {
+     new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
+     # new.pkg <- pkg
+     if (length(new.pkg)) {
+         if (repository == "CRAN") {
+             install.packages(new.pkg, dependencies = TRUE)
+         }
+         if (repository == "Bioconductor") {
+             source("https://bioconductor.org/biocLite.R")
+             biocLite(new.pkg, dependencies = TRUE, ask = FALSE)
+         }
+         if (repository == "github") {
+             devtools::install_github(new.pkg, build_vignettes = FALSE, dependencies = TRUE)
+         }
+     }
+ }
>
> # CRAN PACKAGES
> cranpackages <- c("bbmle", "broom", "cobs", "cowplot", "data.table", "devtools",
+     "doParallel", "dplyr", "drc", "DrImpute", "fastICA", "fitdistrplus", "foreach",
+     "gamlss.dist", "ggExtra", "ggplot2", "ggthemes", "grDevices", "glmnet",
+     "grid", "gtools", "Hmisc", "kernlab", "MASS", "matrixStats", "mclust", "methods",
+     "minpack.lm", "moments", "msir", "NBPSeq", "nonnest2", "parallel", "penalized",
+     "plyr", "pscl", "reshape2", "ROCR", "Rtsne", "scales", "Seurat", "snow",
+     "stats", "tibble", "tidyr", "VGAM", "ZIM")
> ipak(cranpackages, repository = "CRAN")
>
> # BIOCONDUCTOR
> biocpackages <- c("AnnotationDbi", "baySeq", "Biobase", "BiocGenerics", "BiocParallel",
+     "DEDS", "DESeq2", "EBSeq", "edgeR", "IHW", "iCOBRA", "limma", "Linnorm",
+     "MAST", "monocle", "NOISeq", "qvalue", "ROTS", "RUVSeq", "S4Vectors", "scater",
+     "scDD", "scde", "scone", "scran", "SCnorm", "SingleCellExperiment", "SummarizedExperiment",
+     "zinbwave")
> ipak(biocpackages, repository = "Bioconductor")
>
> # GITHUB
> githubpackages <- c("nghiavtr/BPSC", "cz-ye/DECENT", "mohuangx/SAVER", "statOmics/zingeR")
> ipak(githubpackages, repository = "github")
Skipping install of 'BPSC' from a github remote, the SHA1 (5a512e5f) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'DECENT' from a github remote, the SHA1 (dd593069) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'SAVER' from a github remote, the SHA1 (1c124ad8) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'zingeR' from a github remote, the SHA1 (c789ae53) has not changed since last install.
  Use `force = TRUE` to force installation
> devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
✔  checking for file ‘/private/var/folders/7r/ns6f04xj55j72y97pvwtwxj0000_2q/T/RtmpnNPrJr/remotesfd02396b0a5c/bvieth-powsimR-c70c819/DESCRIPTION’ ...
─  preparing ‘powsimR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘powsimR_1.1.4.tar.gz’ (5.3s)

Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘powsimR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so':
  dlopen(/usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
  Referenced from: /usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so
  Reason: image not found
ERROR: lazy loading failed for package ‘powsimR’
* removing ‘/usr/local/lib/R/3.5/site-library/powsimR’
Error in i.p(...) :
  (converted from warning) installation of package ‘/var/folders/7r/ns6f04xj55j72y97pvwtwxj0000_2q/T//RtmpnNPrJr/filefd0229d84453/powsimR_1.1.4.tar.gz’ had non-zero exit status

[swvanderlaan]

And the strangest of things: lpsymphony is really there.

ls -lh /usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/
total 8616
-rwxr-xr-x  1 svanderlaan  5000   4.2M Mar  6 11:42 lpsymphony.so

So I don't get it...

[bvieth]

Dear Sander,

Have you already changed the DLL settings and ulimit as explained in the README on github ?

Best
Beate

[swvanderlaan]

Yes. And this didn't solve it. It really has to do with how macOS Mojave 10.14.3 handles openMP. This is vital to installing lpsymphony and IHW. I don't know how to solve this. I have been scrolling Google, for instance:

• http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/
• https://stackoverflow.com/questions/43595457/alternate-compiler-for-installing-r-packages-clang-error-unsupported-option
• https://github.com/Homebrew/homebrew-science/issues/1304
• https://daijiang.name/en/2017/06/21/fopenmp-option-of-clang-error/
• https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#macOS

But none of this works so far. I still get an error with respect to openMP.

:-(

So when I do the following:

$ R

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin18.2.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocManager::install("lpsymphony", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'lpsymphony'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/lpsymphony_1.10.0.tar.gz'
Content type 'application/x-gzip' length 29147976 bytes (27.8 MB)
==================================================
downloaded 27.8 MB

* installing *source* package ‘lpsymphony’ ...
* Using the default compiler
configure: loading site script /private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/share/config.site

[... I excluded 'millions' of lines of codes ...]

clang++ -DHAVE_CONFIG_H -I. -I../include -I../include -I../Applications/USER/include -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglAllDifferent -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglClique -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglDuplicateRow -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglFlowCover -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglGMI -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglGomory -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglKnapsackCover -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglLandP -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglLiftAndProject -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglMixedIntegerRounding -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglMixedIntegerRounding2 -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglOddHole -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglPreProcess -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglProbing -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglRedSplit -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglRedSplit2 -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglResidualCapacity -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglSimpleRounding -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglTwomir -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src/CglZeroHalf -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Cgl/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Clp/src/OsiClp -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Clp/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Osi/src/Osi -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/CoinUtils/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Clp/src/OsiClp -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Clp/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Osi/src/Osi -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/CoinUtils/src -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/Osi/src/Osi -I/private/var/folders/hk/7x9pbh313hz8hyfdbwqkgc4c0000gn/T/RtmpTgYZHy/R.INSTALLa0da6e5bfa2c/lpsymphony/src/SYMPHONY/CoinUtils/src -D__OSI_CLP__ -DUSE_CGL_CUTS -DSIGHANDLER -DHAS_RANDOM -DHAS_SRANDOM -D__NONE__ -D__DARWIN -DCOMPILE_IN_CG -DCOMPILE_IN_CP -DCOMPILE_IN_LP -DCOMPILE_IN_TM -w -g -O2 -DSYMPHONY_BUILD -fopenmp -c Master/master.c  -fno-common -DPIC -o libSym_la-master.o
clang: error: unsupported option '-fopenmp'
make[3]: *** [libSym_la-master.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/usr/local/lib/R/3.5/site-library/lpsymphony’
* restoring previous ‘/usr/local/lib/R/3.5/site-library/lpsymphony’

[tiagobrc]

also facing the same issue

[jacob-roth]

I've got something similar:

install.packages("~/VGAM_1.1-1.tgz")

and then I get

.
.
.
Creating a new generic function for ‘Rank’ in package ‘VGAM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘VGAM’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/3.6/site-library/00LOCK-VGAM/00new/VGAM/libs/VGAM.so':
  dlopen(/usr/local/lib/R/3.6/site-library/00LOCK-VGAM/00new/VGAM/libs/VGAM.so, 6): Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libquadmath.0.dylib
  Referenced from: /usr/local/lib/R/3.6/site-library/00LOCK-VGAM/00new/VGAM/libs/VGAM.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/3.6/site-library/VGAM’
Warning in install.packages :
  installation of package ‘VGAM’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/10/y7z26t512kbbfrsj12fx3wkr0000gn/T/RtmpC76o60/downloaded_packages’

[bvieth]

Hello,

I am sorry that you encountered these issues. IHW is from bioconductor and I also encounter issues installing these dependencies, particularly after major releases in spring and autumn.
Unfortunately, I can not reconstruct these errors on my Ubuntu machine and have no MAC to test this out.

Kind regards
Beate