Issue installing BPCell on Windows RStudio

[sentisci]

When I am trying to install BPCell, It throws following error

_-- R CMD build --------------------------------------------------------------------------------------------------------------------------------
v checking for file 'C:\Users\sindiris\Documents\R\R-4.1.3\library\BPCells/DESCRIPTION' (359ms)

• preparing 'BPCells': (669ms)
  v checking DESCRIPTION meta-information ...
• cleaning src
• checking for LF line-endings in source and make files and shell scripts (369ms)
• checking for empty or unneeded directories
• building 'BPCells_0.1.0.tar.gz'
  Warning: file 'BPCells/cleanup' did not have execute permissions: corrected
  Warning: file 'BPCells/configure' did not have execute permissions: corrected

Running "C:/Users/sindiris/Documents/R/R-4.1.3/bin/x64/Rcmd.exe" INSTALL
"C:\Users\sindiris\AppData\Local\Temp\1\Rtmp61cBHj/BPCells_0.1.0.tar.gz" --install-tests

• installing to library 'C:/Users/sindiris/Documents/R/R-4.1.3/library'
• installing source package 'BPCells' ...
  ** using staged installation
  Testing hdf5 by compiling example program...
  tools/h5write.c:19:10: fatal error: hdf5.h: No such file or directory
  #include "hdf5.h"
  ^~~~~~~~
  compilation terminated.

Retrying without -lsz flag...
tools/h5write.c:19:10: fatal error: hdf5.h: No such file or directory
#include "hdf5.h"
^~~~~~~~
compilation terminated.

Unable to locate libhdf5. Please install manually or edit compiler flags.
ERROR: configuration failed for package 'BPCells'

• removing 'C:/Users/sindiris/Documents/R/R-4.1.3/library/BPCells'
• restoring previous 'C:/Users/sindiris/Documents/R/R-4.1.3/library/BPCells'
  Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:
  ! System command 'Rcmd.exe' failed

Exit status: 1
stdout & stderr:

Type .Last.error to see the more details._

---

Then I changed hfwrite.c file by including the complete path of the HDF5 library like below
#include "C:/Program Files/HDF_Group/HDF5/1.14.1/include/hdf5.h"
Then I am getting the following issue

-- R CMD build --------------------------------------------------------------------------------------------------------------------------------
v checking for file 'C:\Users\sindiris\Documents\R\R-4.1.3\library\BPCells/DESCRIPTION' (345ms)

• preparing 'BPCells': (658ms)
  v checking DESCRIPTION meta-information ...
• cleaning src
• checking for LF line-endings in source and make files and shell scripts (380ms)
• checking for empty or unneeded directories
• building 'BPCells_0.1.0.tar.gz'
  Warning: file 'BPCells/cleanup' did not have execute permissions: corrected
  Warning: file 'BPCells/configure' did not have execute permissions: corrected

Running "C:/Users/sindiris/Documents/R/R-4.1.3/bin/x64/Rcmd.exe" INSTALL
"C:\Users\sindiris\AppData\Local\Temp\1\Rtmp61cBHj/BPCells_0.1.0.tar.gz" --install-tests

• installing to library 'C:/Users/sindiris/Documents/R/R-4.1.3/library'
• installing source package 'BPCells' ...
  ** using staged installation
  Testing hdf5 by compiling example program...
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lhdf5
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lsz
  collect2.exe: error: ld returned 1 exit status

Retrying without -lsz flag...
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lhdf5
collect2.exe: error: ld returned 1 exit status

Unable to locate libhdf5. Please install manually or edit compiler flags.
ERROR: configuration failed for package 'BPCells'

• removing 'C:/Users/sindiris/Documents/R/R-4.1.3/library/BPCells'
• restoring previous 'C:/Users/sindiris/Documents/R/R-4.1.3/library/BPCells'
  Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:
  ! System command 'Rcmd.exe' failed

Exit status: 1
stdout & stderr:

---

It looks like BPCell is not able to locate "C:\Program Files\HDF_Group\HDF5\1.14.1\lib" path . Can you please help me resolve this ? Where can I declare (by using a global variable or sthng) the above path so that its visible to BPCell. ?

Following is my session info

sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] Rcpp_1.0.11 pillar_1.9.0 compiler_4.1.3 later_1.3.1 urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 [8] remotes_2.4.2.1 tools_4.1.3 digest_0.6.33 pkgbuild_1.4.2 pkgload_1.3.2.1 memoise_2.0.1 lifecycle_1.0.3 [15] tibble_3.2.1 pkgconfig_2.0.3 rlang_1.1.1 shiny_1.7.4.1 cli_3.6.1 rstudioapi_0.15.0 fastmap_1.1.1 [22] stringr_1.5.0 desc_1.4.2 fs_1.6.3 htmlwidgets_1.6.2 vctrs_0.6.3 devtools_2.4.5 rprojroot_2.0.3 [29] glue_1.6.2 R6_2.5.1 processx_3.8.1 fansi_1.0.4 sessioninfo_1.2.2 callr_3.7.3 purrr_1.0.2 [36] magrittr_2.0.3 ps_1.7.5 promises_1.2.1 ellipsis_0.3.2 htmltools_0.5.5 usethis_2.2.2 mime_0.12 [43] xtable_1.8-4 httpuv_1.6.11 utf8_1.2.3 stringi_1.7.12 miniUI_0.1.1.1 cachem_1.0.8 crayon_1.5.2
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[bnprks]

Have you already installed Rtools as described here? This is required for package compilation on Windows. Rtools comes with a copy of hdf5 that it will use automatically

[sentisci]

The link is helpful. Using R-4.3. and Rtools43 I was able to install BPCells. Thanks much for the help