Issue with installing NicheMapR

[I-Hickman]

Hello,

I am having trouble installing NicheMapR to my mac. I have tried to install it through the multiple ways that are listed on the NicheMap website:

1. Install the latest release of NicheMapR, go to the NicheMapR releases page

install.packages("NicheMapR_3.1.0.tgz", repos = NULL,

•              type = .Platform$pkgType)
  

library(NicheMapR)
Error: package or namespace load failed for ‘NicheMapR’:
package ‘NicheMapR’ was installed before R 4.0.0: please re-install it

2. To install NicheMapR from source via github you will need the devtools package for R as well as a Fortran compiler for your platform. I downloaded gfortran-ARM-12.1-Monterey.dmg for Apple Silicon computers. Then tried to run the script.

install.packages('devtools')
Error in install.packages : Updating loaded packages

Restarting R session...

install.packages("devtools")
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.1/devtools_2.4.4.tgz'
Content type 'application/x-gzip' length 422640 bytes (412 KB)
==================================================
downloaded 412 KB

The downloaded binary packages are in
/var/folders/qn/rg86xsy10x97896c5xhgxx280000gn/T//RtmpwOExSH/downloaded_packages

library(devtools)
Loading required package: usethis
Warning messages:
1: package ‘devtools’ was built under R version 4.1.1
2: package ‘usethis’ was built under R version 4.1.1
devtools::install_github('mrke/NicheMapR')
Downloading GitHub repo mrke/NicheMapR@HEAD
✔ checking for file ‘/private/var/folders/qn/rg86xsy10x97896c5xhgxx280000gn/T/RtmpwOExSH/remotes66d751fbab98/mrke-NicheMapR-cd40f0b/DESCRIPTION’ ...
─ preparing ‘NicheMapR’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘NicheMapR_3.2.0.tar.gz’

• installing source package ‘NicheMapR’ ...
  ** using staged installation
  ** libs
  /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c AACOMMONDAT.f -o AACOMMONDAT.o
  make: /opt/R/arm64/bin/gfortran: No such file or directory
  make: *** [AACOMMONDAT.o] Error 1
  ERROR: compilation failed for package ‘NicheMapR’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/NicheMapR’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/NicheMapR’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/qn/rg86xsy10x97896c5xhgxx280000gn/T//RtmpwOExSH/file66d77d38f90e/NicheMapR_3.2.0.tar.gz’ had non-zero exit status

Any help on what I should do would be greatly appreciated!
Thanks

[emiliamrl]

Hi, I also had issues installing. After installing Rtools I could install the package using the package remotes.
remotes::install_github("mrke/NicheMapR")

[diogoprov]

Same thing here, either with remotes or devtools I keep getting the same error message:

gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c AACOMMONDAT.f -o AACOMMONDAT.o
gfortran-4.2: error trying to exec '/usr/local/bin/i686-apple-darwin8-gfortran-4.2': execvp: Bad CPU type in executable
make: *** [AACOMMONDAT.o] Error 255
ERROR: compilation failed for package ‘NicheMapR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/NicheMapR’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/yz/9m219xy93sq0cfrsg73gxckr0000gn/T//RtmpKzyRXf/filee8d71410b89/NicheMapR_3.2.0.tar.gz’ had non-zero exit status

I'm using

> R.Version()$version.string; R.Version()$platform
[1] "R version 4.2.1 (2022-06-23)"
[1] "x86_64-apple-darwin17.0"

on a MacBook Pro 2021 with M1 chip running macOS 12.5.1.

Appreciate any help

Thank you in advance,
Diogo

[diogoprov]

Even after updating the gfortran compiler [follow the advice here], I couldn't get it to work, I now get a different error message:

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: ignoring file AACOMMONDAT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ABOVEGROUND.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ADJREC.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file BELOWGROUND.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file BLKDATA.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file BREED.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file BURROWIN.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file COND.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file CONV.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file COMMONDAT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file BTRFLGEOM.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file CONV_ENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DCHXY.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEB_EULER.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEB_BABY.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEB_HOLO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEXPI.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DEVRESET.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_AELES.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_AVELHS.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_ELH.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_EEES.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_PSI.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DRYAIR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ERRMSG.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file EVAP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file EVALXZ.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DGET_DEB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file FUN.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file GEOM.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file FUNC.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file GEOM_ENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file FUNSKIN.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ECTOTHERM.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file GAMMA.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file IOSOLR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64

ld: warning: ld: warning: ignoring file FUNWING.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ld: warning: ignoring file DOPRI5.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: 
ignoring file INFIL.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ignoring file GETKFUR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file MICRO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file DSUB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ISPLINE.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ignoring file IRPROP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ONELUMP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file MICROSEGMT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file OSUB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file MET.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file PHOTOPERIOD.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file QROMB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file MICROCLIMATE.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: 
ld: warning: ignoring file RADIN.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64


ld: warning: ld: warning: ignoring file RADOUT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file RELHUMID.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file RESP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64


ignoring file PARECT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SELDEP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: 
ignoring file RYTREC.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SEAWATER.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file RESPFUN.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SHADEADJUST.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ignoring file POLINT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SFODE.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file SINEC.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SNOWLAYER.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64

ld: warning: ignoring file SIMULSOL.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file SOLAR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ld: warning: ignoring file SOLRAD.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SEVAP_ENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SOLVENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SOLAR_ENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file SOILPROPS.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64

ld: warning: ignoring file TAB.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file THERMO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ld: warning: ignoring file TIMCON.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ld: warning: ignoring file SPLINE.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ignoring file SEVAP.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64


ld: warning: ignoring file TRAPHR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file VAPPRS.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ld: warning: ignoring file WETAIR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file ZBRAC.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file WING_SOLAR.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ignoring file WINGS.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64ignoring file SOLOUT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file VSINE.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64

ld: warning: ignoring file ZBRENT_ENDO.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file WATER.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ld: warning: ignoring file gads.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: warning: ignoring file TRAPZD.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ignoring file ZBRENT.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
ld: malformed universal file: slice content is not mach-o or a static library file '/usr/local/lib/libgfortran.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [NicheMapR.so] Error 1
ERROR: compilation failed for package ‘NicheMapR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/NicheMapR’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/yz/9m219xy93sq0cfrsg73gxckr0000gn/T//RtmppUwIos/file24c26d0ba1ab/NicheMapR_3.2.0.tar.gz’ had non-zero exit status

[mrke]

Diogo - make sure you delete the .o files before you try and recompile

[diogoprov]

Thanks @mrke ! Somehow I got it to work on a different, new computer. Thanks