Error in state$requirements[[record$Package]] #983

nick-youngblut · 2022-04-13T12:39:08Z

reprex:

conda install -y r-base=4.0.2 r-renv
R -e 'renv::install("nick-youngblut/endoR")'

error:

Retrieving 'https://api.github.com/repos/nick-youngblut/endoR/tarball/abe0efd3796701d888737d22795955c81dae9534' ...
	OK [downloaded 781.5 Kb in 0.6 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/data.table_1.14.2.tar.gz' ...
	OK [downloaded 5.1 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/dplyr_1.0.8.tar.gz' ...
	OK [downloaded 860.1 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/generics_0.1.2.tar.gz' ...
	OK [downloaded 120.4 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/glue_1.6.2.tar.gz' ...
	OK [downloaded 104 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.1.tar.gz' ...
	OK [downloaded 97.4 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/rlang_1.0.2.tar.gz' ...
	OK [downloaded 707.8 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/magrittr_2.0.3.tar.gz' ...
	OK [downloaded [26](https://github.com/nick-youngblut/endoR/runs/6007299966?check_suite_focus=true#step:5:26)0.8 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' ...
	OK [downloaded 61.9 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/tibble_3.1.6.tar.gz' ...
	OK [downloaded 722 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/ellipsis_0.3.2.tar.gz' ...
	OK [downloaded 7.9 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/fansi_1.0.3.tar.gz' ...
	OK [downloaded 469.9 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/pillar_1.7.0.tar.gz' ...
	OK [downloaded 517.3 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.8.3.tar.gz' ...
	OK [downloaded 2.9 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/ggforce_0.3.3.tar.gz' ...
	OK [downloaded 838 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/tweenr_1.0.2.tar.gz' ...
	OK [downloaded 555.3 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz' ...
	OK [downloaded 77.8 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.9.2.tar.gz' ...
	OK [downloaded 1.4 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/igraph_1.3.0.tar.gz' ...
	OK [downloaded 2.4 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/ggrepel_0.9.1.tar.gz' ...
	OK [downloaded 265 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/viridis_0.6.2.tar.gz' ...
	OK [downloaded 2.9 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/gridExtra_2.3.tar.gz' ...
	OK [downloaded 1 Mb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/tidygraph_1.2.1.tar.gz' ...
	OK [downloaded 115.4 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/tidyr_1.2.0.tar.gz' ...
	OK [downloaded 7[27](https://github.com/nick-youngblut/endoR/runs/6007299966?check_suite_focus=true#step:5:27).1 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/cpp11_0.4.2.tar.gz' ...
	OK [downloaded [31](https://github.com/nick-youngblut/endoR/runs/6007299966?check_suite_focus=true#step:5:31)0.3 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/graphlayouts_0.8.0.tar.gz' ...
	OK [downloaded 2.3 Mb in 0.2 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.11.0.0.0.tar.gz' ...
	OK [downloaded 1.3 Mb in 0.1 secs]
Error in state$requirements[[record$Package]] : 
  wrong arguments for subsetting an environment
Calls: <Anonymous> ... handler -> renv_retrieve_impl -> renv_retrieve_incompatible
Traceback (most recent calls last):
11: renv::install("nick-youngblut/endoR")
10: retrieve(names(remotes))
 9: handler(package, renv_retrieve_impl(package))
 8: renv_retrieve_impl(package)
 7: renv_retrieve_github(record)
 6: renv_retrieve_package(record, url, path)
 5: renv_retrieve_successful(record, path)
 4: retrieve(package)
 3: handler(package, renv_retrieve_impl(package))
 2: renv_retrieve_impl(package)
 1: renv_retrieve_incompatible(record)
Execution halted
Error: Process completed with exit code 1.

The issue seems similar to #955.

Due to the inTrees package, I can't just use a more up-to-date version of R.

The text was updated successfully, but these errors were encountered:

kevinushey · 2022-04-13T17:08:23Z

Can you please install the latest development version of renv, and let me know what error message you see then?

nick-youngblut · 2022-04-13T19:19:18Z

I couldn't:

The downloaded source packages are in
	‘/tmp/RtmpvDex3g/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
✔  checking for file ‘/tmp/RtmpvDex3g/remotes3f1f66cc6989/r-lib-devtools-5687588/DESCRIPTION’ (5.7s)
─  preparing ‘devtools’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘devtools_2.4.3.9000.tar.gz’

ERROR: dependency ‘pkgdown’ is not available for package ‘devtools’
* removing ‘/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/devtools’
Warning messages:
1: In i.p(...) :
  installation of package ‘textshaping’ had non-zero exit status
2: In i.p(...) : installation of package ‘ragg’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘pkgdown’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘/tmp/RtmpvDex3g/file3f1f7ef297c7/devtools_2.4.3.9000.tar.gz’ had non-zero exit status

I used devtools::install_github("r-lib/devtools")

kevinushey · 2022-04-13T19:49:06Z

The development version of renv, not devtools.

nick-youngblut · 2022-04-14T07:37:48Z

Whoops. My bad... to much multi-tasking.

I created a new env:

conda install -y r-base=4.0.2 r-renv
R -e 'renv::install("rstudio/renv")'
R -e 'renv::install("nick-youngblut/endoR")'

...and using the dev version of renv resulted in:

> renv::install("nick-youngblut/endoR")
Retrieving 'https://api.github.com/repos/nick-youngblut/endoR/tarball/abe0efd3796701d888737d22795955c81dae9534' ...
	OK [downloaded 781.5 Kb in 0.4 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/data.table_1.14.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/dplyr_1.0.8.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/generics_0.1.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/glue_1.6.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/rlang_1.0.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/magrittr_2.0.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/tibble_3.1.6.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/ellipsis_0.3.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/fansi_1.0.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/pillar_1.7.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/cli_3.2.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/crayon_1.5.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/utf8_1.2.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/vctrs_0.4.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/tidyselect_1.1.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/purrr_0.3.4.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.5.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/digest_0.6.29.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/gtable_0.3.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/isoband_0.2.5.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/MASS_7.3-56.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/mgcv_1.8-40.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/Matrix_1.4-1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/lattice_0.20-45.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/nlme_3.1-157.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/scales_1.2.0.tar.gz' ...
	OK [downloaded 263.9 Kb in 0.1 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/farver_2.1.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/labeling_0.4.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/colorspace_2.0-3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/viridisLite_0.4.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/withr_2.5.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/ggraph_2.0.5.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.8.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/ggforce_0.3.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/tweenr_1.0.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.9.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/igraph_1.3.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/ggrepel_0.9.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/viridis_0.6.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/gridExtra_2.3.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/tidygraph_1.2.1.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/tidyr_1.2.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/cpp11_0.4.2.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/graphlayouts_0.8.0.tar.gz' ...
	OK [file is up to date]
Retrieving 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.11.0.0.0.tar.gz' ...
	OK [file is up to date]
Error: failed to find source for 'inTrees' in package repositories
Traceback (most recent calls last):
15: renv::install("nick-youngblut/endoR")
14: retrieve(names(remotes))
13: handler(package, renv_retrieve_impl(package))
12: renv_retrieve_impl(package)
11: renv_retrieve_github(record)
10: renv_retrieve_package(record, url, path)
 9: renv_retrieve_successful(record, path)
 8: retrieve(package)
 7: handler(package, renv_retrieve_impl(package))
 6: renv_retrieve_impl(package)
 5: records[[package]] %||% renv_retrieve_missing_record(package)
 4: renv_retrieve_missing_record(package)
 3: renv_available_packages_entry(package, type = "source")
 2: stopf(fmt, type, pkgver)
 1: stop(sprintf(fmt, ...), call. = call.)
Execution halted

Since inTrees has been removed from CRAN, I had to install it via github:

renv::install("softwaredeng/inTrees/inTrees.Rcheck/inTrees")

...which then got me closer with R -e 'renv::install("nick-youngblut/endoR")':

Installing nloptr [2.0.0] ...
	FAILED
Error installing package 'nloptr':
==================================

* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 accepts -g... (cached) yes
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
using NLopt via local cmake build on x86_64
set CMAKE_BIN=/usr/bin/cmake
set CC=x86_64-conda_cos6-linux-gnu-cc
set CFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix
set CXX=x86_64-conda_cos6-linux-gnu-c++
set CXXFLAGS=-std=gnu++11 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix
set LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -L/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib
CMake Error: The source directory "/tmp/RtmpChk5HF/R.INSTALL10cbb63ef0891/nloptr/src/nlopt-build" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
Unknown argument -j
Unknown argument 2
Usage: cmake --build <dir> [options] [-- [native-options]]
Options:
  <dir>          = Project binary directory to be built.
  --target <tgt> = Build <tgt> instead of default targets.
                   May only be specified once.
  --config <cfg> = For multi-configuration tools, choose <cfg>.
  --clean-first  = Build target 'clean' first, then build.
                   (To clean only, use --target 'clean'.)
  --use-stderr   = Ignored.  Behavior is default in CMake >= 3.0.
  --             = Pass remaining options to the native tool.
CMake Error: The source directory "/tmp/RtmpChk5HF/R.INSTALL10cbb63ef0891/nloptr/src/nlopt" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
x86_64-conda_cos6-linux-gnu-cc -I"/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/include" -DNDEBUG -I../inst/include  -I'/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/.renv/1/testthat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib   -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix  -c init_nloptr.c -o init_nloptr.o
x86_64-conda_cos6-linux-gnu-cc -I"/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/include" -DNDEBUG -I../inst/include  -I'/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/.renv/1/testthat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib   -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix  -c nloptr.c -o nloptr.o
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/include" -DNDEBUG -I../inst/include  -I'/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/.renv/1/testthat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix  -c test-C-API.cpp -o test-C-API.o
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/include" -DNDEBUG -I../inst/include  -I'/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/.renv/1/testthat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -I/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST=/usr/local/src/conda-prefix  -c test-runner.cpp -o test-runner.o
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -L/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -Wl,-rpath-link,/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lgomp -lquadmath -lpthread -Lnlopt/lib -lnlopt -L/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/lib -lR
/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lnlopt
collect2: error: ld returned 1 exit status
make: *** [/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/share/make/shlib.mk:6: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/lib/R/library/.renv/1/nloptr’
Error: install of package 'nloptr' failed [error code 1]
Traceback (most recent calls last):
11: renv::install("nick-youngblut/endoR")
10: renv_install_impl(records)
 9: renv_install_staged(records)
 8: renv_install_default(records)
 7: handler(package, renv_install_package(record))
 6: renv_install_package(record)
 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })
 4: renv_install_package_impl(record)
 3: r_cmd_install(package, path)
 2: r_exec_error(package, output, "install", status)
 1: stop(error)
Execution halted

Installing nloptr via conda and then re-running R -e 'renv::install("nick-youngblut/endoR")' resulted in a successful install.

I'll probably switch the install to a more conda-focused method:

mamba install -y r-base=4.0.2 r-renv r-nloptr r-data.table r-dplyr r-ggplot2 r-ggraph r-igraph r-stringr
R -e 'renv::install("rstudio/renv")'
R -e 'renv::install("softwaredeng/inTrees/inTrees.Rcheck/inTrees")'
R -e 'renv::install("nick-youngblut/endoR")'

kevinushey · 2022-04-14T16:28:44Z

That seems more like a conda issue rather than an renv issue.

/tmp/global2/nyoungblut/code/HUBIF_cophylo/conda_envs/TEST/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lnlopt
collect2: error: ld returned 1 exit status

I'm not sure what the solution is here to make sure libnlopt.so is visible during compilation in conda.

lorenzwalthert mentioned this issue Jun 28, 2022

precommit fails to set up environment after upgrade to R 4.2.1 lorenzwalthert/precommit#424

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hadley closed this as completed Apr 26, 2023

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Error in state$requirements[[record$Package]] #983

Error in state$requirements[[record$Package]] #983

nick-youngblut commented Apr 13, 2022

kevinushey commented Apr 13, 2022

nick-youngblut commented Apr 13, 2022

kevinushey commented Apr 13, 2022

nick-youngblut commented Apr 14, 2022 •

edited

kevinushey commented Apr 14, 2022

Error in state$requirements[[record$Package]] #983

Error in state$requirements[[record$Package]] #983

Comments

nick-youngblut commented Apr 13, 2022

reprex:

error:

kevinushey commented Apr 13, 2022

nick-youngblut commented Apr 13, 2022

kevinushey commented Apr 13, 2022

nick-youngblut commented Apr 14, 2022 • edited

kevinushey commented Apr 14, 2022

nick-youngblut commented Apr 14, 2022 •

edited