error when building from source

[KaiWaldrant]

We're having trouble again with installing the package when building from source:

#6 26.94 Downloading GitHub repo welch-lab/RcppPlanc@HEAD
#6 28.83 
#6 28.83 Running `R CMD build`...
#6 29.10 * checking for file ‘/tmp/RtmpsP9Wju/remotes3d3301f6cd5/welch-lab-RcppPlanc-d26af1d/DESCRIPTION’ ... OK
#6 29.10 * preparing ‘RcppPlanc’:
#6 29.10 * checking DESCRIPTION meta-information ... OK
#6 29.10 * cleaning src
#6 29.10 * running ‘cleanup’
#6 29.10 * checking for LF line-endings in source and make files and shell scripts
#6 29.10 * checking for empty or unneeded directories
#6 29.10 * building ‘RcppPlanc_1.0.0.tar.gz’
#6 29.10 Installing package into ‘/usr/local/lib/R/site-library’
#6 29.10 (as ‘lib’ is unspecified)
#6 29.27 * installing *source* package ‘RcppPlanc’ ...
#6 29.27 ** using staged installation
#6 29.76 ./configure: 47: Syntax error: Unterminated quoted string
#6 29.76 ERROR: configuration failed for package ‘RcppPlanc’
#6 29.76 * removing ‘/usr/local/lib/R/site-library/RcppPlanc’
#6 29.78 Warning message:
#6 29.78 In i.p(...) :
#6 29.78   installation of package ‘/tmp/RtmpsP9Wju/file3d359a14f15/RcppPlanc_1.0.0.tar.gz’ had non-zero exit status

sessioninfo():

R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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: UTC
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.3.3 bspm_0.5.5.1 

[theAeon]

My bad-noticed that typo yesterday and forgot to push the fix to github. Try it again.

[KaiWaldrant]

It is fixed.

We wanted to replace the source install with cmd below and it installed with no error:

install.packages("RcppPlanc", repos = c(
linux = 'https://welch-lab.r-universe.dev/bin/linux/jammy/4.3',
sources = 'https://welch-lab.r-universe.dev',
cran = 'https://cloud.r-project.org'))

But when running our script (https://github.com/openproblems-bio/openproblems-v2/blob/main/src/tasks/batch_integration/methods/liger/script.R) we still got an error message that the package was not installed:

Error in `.runINMF.list()`:
! Package RcppPlanc is required for iNMF integration. Please install it by command: `devtools::install_github('welch-lab/RcppPlanc')`

[theAeon]

If the build was failing due to a typo for you, it was likely failing on r-universe as well. Glad to hear it works.

---

From: Kai Waldrant @.> Sent: Wednesday, April 3, 2024 9:28:28 AM To: welch-lab/RcppPlanc @.> Cc: Robbins, Andrew @.>; Comment @.> Subject: Re: [welch-lab/RcppPlanc] error when building from source (Issue #4)

External Email - Use Caution

It is fixed.

We wanted to replace the source install with and got no installation error:

install.packages("RcppPlanc", repos = c( linux = 'https://welch-lab.r-universe.dev/bin/linux/jammy/4.3', sources = 'https://welch-lab.r-universe.dev', cran = 'https://cloud.r-project.org'))

But when running our script (https://github.com/openproblems-bio/openproblems-v2/blob/main/src/tasks/batch_integration/methods/liger/script.R) we still got an error message that the package was not installed:

Error in .runINMF.list(): ! Package RcppPlanc is required for iNMF integration. Please install it by command: devtools::install_github('welch-lab/RcppPlanc')

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