I've downloaded the ComplexHeatmap function many of times before, but this is the first time I've seen this error message. It comes up after I try the following code, then try running the library command. R version is 4.0.0.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap", force = TRUE)
install.packages('modeltools')
> library(ComplexHeatmap)
Error: package or namespace load failed for ‘ComplexHeatmap’:
.onLoad failed in loadNamespace() for 'Cairo', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/nathan.laspina/Documents/R/win-library/4.0/Cairo/libs/x64/Cairo.dll':
LoadLibrary failure: The specified procedure could not be found.
In addition: Warning message:
package ‘ComplexHeatmap’ was built under R version 4.0.3
It seems like it just got saved to the wrong place, how can I change that location?
>BiocManager::install("ComplexHeatmap", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.12 (BiocManager 1.30.18), R 4.0.0 (2020-04-24)
Installing package(s) 'ComplexHeatmap'
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/ComplexHeatmap_2.6.2.zip'
Content type 'application/zip' length 3286900 bytes (3.1 MB)
downloaded 3.1 MB
package ‘ComplexHeatmap’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\...\AppData\Local\Temp\1\RtmpWwrYJX\downloaded_packages
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.0.0/library
packages:
boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
nnet, rpart, spatial, survival
Old packages: 'cli', 'dbplyr', 'dplyr', 'tibble'
Update all/some/none? [a/s/n]:
Thank you. A quick question about upgrading to a newer version of R, if I may. I thought one should always stay 1 version behind because newer versions tend to have more issues with bug/crashes. Is that not true?
That's not my experience. I always upgrade to the new version of R/BioC on the day it's released, and I've never thought it was a bad idea because of bugs. And I use R all day every day, so I imagine if there were consistent problems I would have noticed them by now.
That said, there may be issues that arise where the maintainer of a package realizes there is a bug (or somebody tells them about it), and they push a fix. But for most packages the bugs are real edge cases that won't arise for most people. Something like
ComplexHeatmap
gets used by thousands of people every day, and if there were a problem you know for sure people would complain and it would get fixed quickly.But anyway, IMO you should upgrade at release, every time.