Hi - I am trying to use bitr and it fails... so I cannot use your code. I am using R 3.5.1.

I tried two ways of loading clusterProfiler:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("clusterProfiler", version = "3.8")

and also this:

source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

And when I run:
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
gene.df <- bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), OrgDb = org.Hs.eg.db)
head(gene.df)

I get this error:

Error in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), : could not find function "bitr"
Traceback:

So then I tried to install bitr directly but I get this:

library(devtools)
install_github("GuangchuangYu/bitr")
Gives the following error:

Downloading GitHub repo GuangchuangYu/bitr@master
from URL https://api.github.com/repos/GuangchuangYu/bitr/zipball/master
Installing bitr
'/gpfs/main/home/aconard/anaconda/envs/mro_env/lib/R/bin/R' --no-site-file
--no-environ --no-save --no-restore --quiet CMD INSTALL
'/tmp/RtmpNaU90m/devtools1c981fc660aa/GuangchuangYu-bitr-246358c'
--library='/gpfs/main/home/aconard/anaconda/envs/mro_env/lib/R/library'
--install-tests

Installation failed: Command failed (1)

Help! Thank you!

I am trying to install clusterProfiler.

Here is my code:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("clusterProfiler")

Error:

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0
(2020-04-24)
Installing package(s) 'clusterProfiler'
also installing the dependency ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/clusterProfiler_3.16.0.tgz'
Content type 'application/x-gzip' length 655209 bytes (639 KB)

downloaded 639 KB

The downloaded binary packages are in
/var/folders/v9/swswf5596ynbqcfdvl8q96s40000gn/T//RtmpQAtwof/downloaded_packages
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GO.db_3.11.1.tar.gz'
Content type 'application/x-gzip' length 33183776 bytes (31.6 MB)

downloaded 31.6 MB

dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 92634 Done echo 'tools:::.install_packages()'
92635 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
‘/private/var/folders/v9/swswf5596ynbqcfdvl8q96s40000gn/T/RtmpQAtwof/downloaded_packages’
Old packages: 'xfun'
Update all/some/none? [a/s/n]:
a

There is a binary version available but the source
version is later:
binary source needs_compilation
xfun 0.13 0.14 FALSE

installing the source package ‘xfun’

trying URL 'https://cran.rstudio.com/src/contrib/xfun_0.14.tar.gz'
Content type 'application/x-gzip' length 69436 bytes (67 KB)

downloaded 67 KB

dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 92653 Done echo 'tools:::.install_packages()'
92654 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
‘/private/var/folders/v9/swswf5596ynbqcfdvl8q96s40000gn/T/RtmpQAtwof/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘xfun’ had non-zero exit status

Any ideas in what I am doing wrong here?

Could some one please tell me how I can get entrezgene_id if I have an input as pathcode+enzymecode?