Installation Fails due to RcppArmadillo
Opened this issue · 1 comments
AtanasiuDemian commented
Hi, thanks for developing this. I'm having an issue with installing due to the following error (Windows 10):
> devtools::install_github('immunogenomics/presto', dependencies=FALSE)
Downloading GitHub repo immunogenomics/presto@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\ademian\AppData\Local\Temp\Rtmp0OQbcy\remotes5fe438e34570\immunogenomics-presto-31dc97f/DESCRIPTION' (372ms)
─ preparing 'presto': (395ms)
✔ 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 'presto_1.0.0.tar.gz'
Installing package into ‘C:/Users/ademian/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
* installing *source* package 'presto' ...
** using staged installation
** libs
using C++ compiler: 'g++ (GCC) 10.2.0'
using C++11
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I'C:/Users/ademian/AppData/Local/R/win-library/4.3/Rcpp/include' -I'C:/Users/ademian/AppData/Local/R/win-library/4.3/RcppArmadillo/include' -I"c:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/ademian/AppData/Local/R/win-library/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:27,
from C:/Users/ademian/AppData/Local/R/win-library/4.3/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
C:/Users/ademian/AppData/Local/R/win-library/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfig.h:110:12: fatal error: RcppArmadillo/config/RcppArmadilloConfigGenerated.h: No such file or directory
110 | #include <RcppArmadillo/config/RcppArmadilloConfigGenerated.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [C:/PROGRA~1/R/R-43~1.3/etc/x64/Makeconf:272: RcppExports.o] Error 1
ERROR: compilation failed for package 'presto'
* removing 'C:/Users/ademian/AppData/Local/R/win-library/4.3/presto'
Warning message:
In i.p(...) :
installation of package ‘C:/Users/ademian/AppData/Local/Temp/RtmpeQsEYJ/file6d0842be5345/presto_1.0.0.tar.gz’ had non-zero exit status
Same error happens when I install with dependencies. Could you please help with this? Below is my session info:
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.3 (2024-02-29 ucrt)
os Windows 10 x64 (build 19045)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United Kingdom.utf8
ctype English_United Kingdom.utf8
tz Europe/London
date 2024-03-11
rstudio 2023.12.1+402 Ocean Storm (desktop)
pandoc NA
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.1)
Biobase * 2.62.0 2023-10-24 [1] Bioconductor
BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.1)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.2)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.2)
DelayedArray 0.28.0 2023-10-24 [1] Bioconductor
GenomeInfoDb * 1.38.5 2023-12-28 [1] Bioconductor 3.18 (R 4.3.2)
GenomeInfoDbData 1.2.11 2024-01-08 [1] Bioconductor
GenomicRanges * 1.54.1 2023-10-29 [1] Bioconductor
IRanges * 2.36.0 2023-10-24 [1] Bioconductor
lattice 0.22-5 2023-10-24 [2] CRAN (R 4.3.3)
Matrix * 1.6-4 2023-11-30 [1] CRAN (R 4.3.2)
MatrixGenerics * 1.14.0 2023-10-24 [1] Bioconductor
matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.3.2)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.2)
RcppArmadillo * 0.12.8.1.0 2024-03-03 [1] CRAN (R 4.3.3)
RCurl 1.98-1.13 2023-11-02 [1] CRAN (R 4.3.2)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.2)
S4Arrays 1.2.0 2023-10-24 [1] Bioconductor
S4Vectors * 0.40.2 2023-11-23 [1] Bioconductor
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.2)
SingleCellExperiment * 1.24.0 2023-10-24 [1] Bioconductor
SparseArray 1.2.3 2023-12-25 [1] Bioconductor 3.18 (R 4.3.2)
SummarizedExperiment * 1.32.0 2023-10-24 [1] Bioconductor
XVector 0.42.0 2023-10-24 [1] Bioconductor
zlibbioc 1.48.0 2023-10-24 [1] Bioconductor
[1] C:/Users/ademian/AppData/Local/R/win-library/4.3
[2] C:/Program Files/R/R-4.3.3/library
slowkow commented
In your log I noticed this error:
fatal error: RcppArmadillo/config/RcppArmadilloConfigGenerated.h: No such file or directory
You might want to try the steps below.
- Close R, start a fresh new R session.
- Re-install RcppArmadillo with
install.packages("RcppArmadillo") - Try installing presto with
devtools::install_github("immunogenomics/presto")
If that doesn't work, let us know what you see.