trljcl commented 4 years ago

Hi, I've moved to a new linux box and am trying to reinstall rcdk using devtools (I need >= 3.4.8 for correct handing of isotope designations in element lists). I did this successfully ~ a year ago on R3.5.0 and am repeating the same procedure now on the new box under r3.6.2 (after first checking all dependencies are installed). rcdklibs installs fine, but rcdk does not - any advice much appreciated!

library("devtools")

install_github("https://github.com/CDK-R/cdkr", subdir="rcdk") Downloading GitHub repo CDK-R/cdkr@master v checking for file '/tmp/RtmpkOtxb2/remotes29b5186eac66/CDK-R-cdkr-049850a/rcdk/DESCRIPTION' (505ms)

preparing 'rcdk': v 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 'rcdk_3.4.9.2.tar.gz' Warning: invalid uid value replaced by that for user 'nobody'

installing source package 'rcdk' ... using staged installation R data inst byte-compile and prepare package for lazy loading 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 'rcdk': object 'do' not found whilst loading namespace 'rcdk' Error: loading failed Execution halted ERROR: loading failed
removing '/shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research1/lib/R/library/rcdk' Error: Failed to install 'rcdk' from GitHub:

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS

Matrix products: default BLAS: /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research1/lib/R/lib/libRblas.so LAPACK: /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research1/lib/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB [7] LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached): [1] compiler_3.6.2 tools_3.6.2

zachcp commented 4 years ago

Sorry, @trljcl , this should be fixed in #101. In the meantime you can try below:

# I can replicate your bug
install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")

# this should work
install_github("https://github.com/zachcp/cdkr", subdir="rcdk", ref="docfixes")

zachcp commented 4 years ago

101 is merged. closing. if the issue persists, feel free to reopen

zachcp commented 4 years ago

@trljcl can you see if this is still an issue and close if its resolved.

CDK-R / cdkr

install failure object 'do' not found whilst loading namespace 'rcdk' #102

101 is merged. closing. if the issue persists, feel free to reopen