Cant install celldex because dependency alabaster cant be installed...

[marencc]

Hi!
I updated R a few days ago and I also updated BiocManager and so... but when trying to install celldex, it's not working... I've tried reinstalling Rcpp, rhd5lib, hdf5, I've tried many things and nothing seems to work. I need your help.

` BiocManager::install("celldex")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installing package(s) 'celldex'
also installing the dependencies ‘alabaster.ranges’, ‘alabaster.base’, ‘alabaster.matrix’, ‘alabaster.se’

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.ranges_1.4.0.tar.gz'
Content type 'application/x-gzip' length 230019 bytes (224 KB)

downloaded 224 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.base_1.4.1.tar.gz'
Content type 'application/x-gzip' length 404498 bytes (395 KB)

downloaded 395 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.matrix_1.4.0.tar.gz'
Content type 'application/x-gzip' length 271307 bytes (264 KB)

downloaded 264 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/alabaster.se_1.4.0.tar.gz'
Content type 'application/x-gzip' length 228542 bytes (223 KB)

downloaded 223 KB

trying URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/celldex_1.14.0.tar.gz'
Content type 'application/x-gzip' length 412271 bytes (402 KB)

downloaded 402 KB

• installing source package ‘alabaster.base’ ...
  ** using staged installation
  ** libs
  using C++ compiler: ‘g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0’
  using C++17
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c check_csv.cpp -o check_csv.o
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I'/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c check_list.cpp -o check_list.o
  In file included from ../inst/include/ritsuko/hdf5/miscellaneous.hpp:7:0,
  from ../inst/include/ritsuko/hdf5/hdf5.hpp:15,
  from ../inst/include/uzuki2/parse_hdf5.hpp:22,
  from ../inst/include/uzuki2/uzuki2.hpp:15,
  from check_list.cpp:3:
  ../inst/include/ritsuko/hdf5/open.hpp:6:10: fatal error: filesystem: No such file or directory
  #include
  ^~~~~~~~~~~~
  compilation terminated.
  /usr/lib/R/etc/Makeconf:204: recipe for target 'check_list.o' failed
  make: *** [check_list.o] Error 1
  ERROR: compilation failed for package ‘alabaster.base’
• removing ‘/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/alabaster.base’
  ERROR: dependency ‘alabaster.base’ is not available for package ‘alabaster.ranges’
• removing ‘/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/alabaster.ranges’
  ERROR: dependency ‘alabaster.base’ is not available for package ‘alabaster.matrix’
• removing ‘/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/alabaster.matrix’
  ERROR: dependencies ‘alabaster.base’, ‘alabaster.ranges’, ‘alabaster.matrix’ are not available for package ‘alabaster.se’
• removing ‘/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/alabaster.se’
  ERROR: dependencies ‘alabaster.base’, ‘alabaster.matrix’, ‘alabaster.se’ are not available for package ‘celldex’
• removing ‘/home/mecc/R/x86_64-pc-linux-gnu-library/4.4/celldex’

The downloaded source packages are in
‘/tmp/RtmpyTPzvp/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
codetools, lattice, MASS, Matrix, nlme, spatial, survival
Warning messages:
1: In install.packages(...) :
installation of package ‘alabaster.base’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘alabaster.ranges’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘alabaster.matrix’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘alabaster.se’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘celldex’ had non-zero exit status
`
sessionInfo()

`sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] patchwork_1.2.0 vctrs_0.6.5 cli_3.6.2
[4] rlang_1.1.3 KernSmooth_2.23-22 generics_0.1.3
[7] ROCR_1.0-11 glue_1.7.0 colorspace_2.1-0
[10] scales_1.3.0 fansi_1.0.6 grid_4.4.0
[13] munsell_0.5.1 tibble_3.2.1 MASS_7.3-60
[16] lifecycle_1.0.4 BiocManager_1.30.23 compiler_4.4.0
[19] RSpectra_0.16-1 dplyr_1.1.4 RColorBrewer_1.1-3
[22] Rcpp_1.0.12 pkgconfig_2.0.3 lattice_0.22-5
[25] R6_2.5.1 RANN_2.6.1 tidyselect_1.2.1
[28] utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
[31] Matrix_1.6-5 tools_4.4.0 gtable_0.3.5
[34] ggplot2_3.5.1
`

[LTLA]

It looks like your compiler toolchain doesn't support the full set of C++17 features (in this case, <filesystem>).

In short, your GCC is too old. It seems that <filesystem> support was implemented in GCC 8, which came out in 2018, so it's been 5 years - I think it's reasonable to expect most people to have a more recent version. R itself also defaults to C++17 (see here) so it's likely that packages other than alabaster.base will be expecting support for C++17 features.

I can't remember what GCC comes with Ubuntu 18, but you might consider upgrading your operating system anyway. Standard support (bugfixes, security updates, etc.) for Ubuntu 18 ran out a year ago.

[Syrest123]

I have experienced the same error but on a server and I don't have sudo rights to upgrade anything...
What should I do?

[LTLA]

I'm afraid you'll just have to use an older version of celldex and Bioconductor.

[Syrest123]

Could you please help with commands I can run to update the GCC on a linux server?

[LTLA]

It's not for the faint of heart. I remember doing this many years ago; pulling down the GCC sources and bootstrapping the builds, then rebuilding R from source, and then finally installing the packages. It was a process that took at least a day of compilation, in addition to a few more days of trial and error to configure it all correctly.

If I were you, I would just ask the server admins to do it for you. They can just do a regular installation of a more up-to-date gcc - I believe any version >10 should be fine - with the system's package manager. If your server uses Lmod, it's easy enough for them to add a new module for this version. They might even be kind enough to re-install R for you.

Otherwise... well, it's been 7 years since C++17 came out, and ~5 years since full support for the specification was implemented in the major compilers. At some point, we've all just got to move on.