Local install, because the package DESCRIPTION can't be parsed

[mdc-webdb]

When I try this:
R -e "pak::pkg_install('local::/mnt/source/Biobase.tar.gz', lib='/tmp/BUILD')"
It fails with:

> pak::pkg_install('local::/mnt/source/Biobase.tar.gz', lib='/tmp/BUILD')
Error: 
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* local::/mnt/source/Biobase.tar.gz: ! pkgdepends resolution error for local::/mnt/source/Biobase.tar.gz.
Caused by error: 
! Line starting 'Biobase/DESCRIPTION ...' is malformed!
---
Backtrace:
1. pak::pkg_install("local::/mnt/source/Biobase.tar.gz", lib = "/tmp/BUILD")
2. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), …
3. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_make_plan", asNamespace("pak"))(...)
3. prop$stop_for_solution_error()
4. private$plan$stop_for_solve_error()
5. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
6. base::throw(new_error("Could not solve package dependencies:\n", msg, …
7. | base::signalCondition(cond)
8. global (function (e) …
Execution halted

But the classic:
R CMD INSTALL --library=/tmp/BUILD /mnt/source/Biobase.tar.gz
will work.
Source for the file:
https://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.72.0.tar.gz
R: 4.6.0
packages:

> installed.packages() 
           Package      LibPath                Version   Priority     
pak        "pak"        "/home/r-build/mein-R" "0.9.5"   NA           
base       "base"       "/usr/lib64/R/library" "4.6.0"   "base"       
boot       "boot"       "/usr/lib64/R/library" "1.3-32"  "recommended"
class      "class"      "/usr/lib64/R/library" "7.3-23"  "recommended"
cluster    "cluster"    "/usr/lib64/R/library" "2.1.8.2" "recommended"
codetools  "codetools"  "/usr/lib64/R/library" "0.2-20"  "recommended"
compiler   "compiler"   "/usr/lib64/R/library" "4.6.0"   "base"       
datasets   "datasets"   "/usr/lib64/R/library" "4.6.0"   "base"       
foreign    "foreign"    "/usr/lib64/R/library" "0.8-91"  "recommended"
graphics   "graphics"   "/usr/lib64/R/library" "4.6.0"   "base"       
grDevices  "grDevices"  "/usr/lib64/R/library" "4.6.0"   "base"       
grid       "grid"       "/usr/lib64/R/library" "4.6.0"   "base"       
KernSmooth "KernSmooth" "/usr/lib64/R/library" "2.23-26" "recommended"
lattice    "lattice"    "/usr/lib64/R/library" "0.22-9"  "recommended"
MASS       "MASS"       "/usr/lib64/R/library" "7.3-65"  "recommended"
Matrix     "Matrix"     "/usr/lib64/R/library" "1.7-5"   "recommended"
methods    "methods"    "/usr/lib64/R/library" "4.6.0"   "base"       
mgcv       "mgcv"       "/usr/lib64/R/library" "1.9-4"   "recommended"
nlme       "nlme"       "/usr/lib64/R/library" "3.1-169" "recommended"
nnet       "nnet"       "/usr/lib64/R/library" "7.3-20"  "recommended"
parallel   "parallel"   "/usr/lib64/R/library" "4.6.0"   "base"       
rpart      "rpart"      "/usr/lib64/R/library" "4.1.27"  "recommended"
spatial    "spatial"    "/usr/lib64/R/library" "7.3-18"  "recommended"
splines    "splines"    "/usr/lib64/R/library" "4.6.0"   "base"       
stats      "stats"      "/usr/lib64/R/library" "4.6.0"   "base"       
stats4     "stats4"     "/usr/lib64/R/library" "4.6.0"   "base"       
survival   "survival"   "/usr/lib64/R/library" "3.8-6"   "recommended"
tcltk      "tcltk"      "/usr/lib64/R/library" "4.6.0"   "base"       
tools      "tools"      "/usr/lib64/R/library" "4.6.0"   "base"       
utils      "utils"      "/usr/lib64/R/library" "4.6.0"   "base"       

[gaborcsardi]

Workaround: name the tar.gz file as a proper R source package, if it is a source package:

> pak::pkg_install("./Biobase.tar.gz")
Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* local::./Biobase.tar.gz: ! pkgdepends resolution error for local::./Biobase.tar.gz.
Caused by error:
! Line starting 'Biobase/DESCRIPTION ...' is malformed!
Type .Last.error to see the more details.

> pak::pkg_install("./Biobase_2.72.0.tar.gz")

→ Will update 1 package.
→ The package (0 B) is cached.
+ Biobase 2.72.0 → 2.72.0 👷🏽‍♀️🔧

[mdc-webdb]

@gaborcsardi yes, this is the problem. But I think that should be fixed.

mv Biobase.tar.gz Biobase_0.0.0.tar.gz
R -e "pak::pkg_install('local::/mnt/source/Biobase_0.0.0.tar.gz', lib='/tmp/BUILD')"
> pak::pkg_install('local::/mnt/source/Biobase_0.0.0.tar.gz', lib='/tmp/BUILD')
✔ Updated metadata database: 4.34 MB in 21 files.
✔ Updating metadata database ... done
 
→ Will install 3 packages.
→ Will download 3 packages with unknown size.
+ Biobase        2.72.0 [bld][cmp][dl]
+ BiocGenerics   0.58.1 [bld][dl]
+ generics       0.1.4  [dl]
  
ℹ Getting 3 pkgs with unknown sizes
✔ Got Biobase 2.72.0 (source) (1.98 MB)
✔ Got generics 0.1.4 (x86_64-redhat-linux-gnu-rhel-9.7) (93.80 kB)
✔ Got BiocGenerics 0.58.1 (source) (58.56 kB)
✔ Installed generics 0.1.4  (50ms)
ℹ Building BiocGenerics 0.58.1
✔ Built BiocGenerics 0.58.1 (4.1s)
✔ Installed BiocGenerics 0.58.1  (58ms)
ℹ Building Biobase 2.72.0
✔ Built Biobase 2.72.0 (7s)
✔ Installed Biobase 2.72.0 (local) (1.1s)
✔ 1 pkg + 2 deps: added 3, dld 3 (2.13 MB) [30.3s]

After all, it works even with a fantasy number.