Failing to find bioconductor packages

[NathanSkene]

When I run

pacman::p_load("BiocStyle",try.bioconductor=TRUE,update.bioconductor=TRUE)

I'm just getting errors about not being able to find the package.

> pacman::p_load("BiocStyle",try.bioconductor=TRUE,update.bioconductor=TRUE)
Installing package into ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/bookdown_0.17.tar.gz'
Content type 'application/x-gzip' length 765923 bytes (747 KB)
==================================================
downloaded 747 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/BiocStyle_2.12.0.tar.gz'
Content type 'application/x-gzip' length 738703 bytes (721 KB)
==================================================
downloaded 721 KB

sh: 1: make -j 8: not found
cat: bookdown.out: No such file or directory
cat: BiocStyle.out: No such file or directory

The downloaded source packages are in
	‘/tmp/RtmpXXWJqU/downloaded_packages’
Installing package into ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Installing package into ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning messages:
1: package ‘BiocStyle’ is not available (for R version 3.6.1) 
2: In p_install(package, character.only = TRUE, ...) : 
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘BiocStyle’
4: package ‘TRUE’ is not available (for R version 3.6.1) 
5: In p_install(package, character.only = TRUE, ...) : 
6: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘TRUE’
7: package ‘TRUE’ is not available (for R version 3.6.1) 
8: In p_install(package, character.only = TRUE, ...) : 
9: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘TRUE’
10: In pacman::p_load("BiocStyle", try.bioconductor = TRUE, update.bioconductor = TRUE) :
  Failed to install/load:
BiocStyle, TRUE, TRUE

[trinker]

I can't reproduce this. Can you try the following without pacman and see what you get:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocStyle")

[NathanSkene]

Thanks for responding (and for developing the package!).

Ran this to confirm I still get the error:

> pacman::p_load("BiocStyle",try.bioconductor=TRUE,update.bioconductor=TRUE)
Installing package into ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Installing package into ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning messages:
1: package ‘TRUE’ is not available (for R version 3.6.1) 
2: In p_install(package, character.only = TRUE, ...) : 
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘TRUE’
4: package ‘TRUE’ is not available (for R version 3.6.1) 
5: In p_install(package, character.only = TRUE, ...) : 
6: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘TRUE’
7: In pacman::p_load("BiocStyle", try.bioconductor = TRUE, update.bioconductor = TRUE) :
  Failed to install/load:
TRUE, TRUE
> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 

Then here's what you suggested I run:

> BiocManager::install("BiocStyle")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'BiocStyle'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/BiocStyle_2.12.0.tar.gz'
Content type 'application/x-gzip' length 738703 bytes (721 KB)
==================================================
downloaded 721 KB

* installing *source* package ‘BiocStyle’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocStyle)

The downloaded source packages are in
	‘/tmp/RtmpVBlcCY/downloaded_packages’
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, survival