Installing: Error: 25:1: unexpected symbol
yancylau opened this issue · 2 comments
yancylau commented
Hi, I tried to install CellChat on R4.0.3 (Linux server, Red Hat), but it raised this error: unexpected symbol. Then I tried to install it on R3.6.3 (Linux server, Red Hat), it gave the same error.
>devtools::install_github("sqjin/CellChat")
Downloading GitHub repo sqjin/CellChat@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: gdtools (0.2.2 -> 0.2.3) [CRAN]
Enter one or more numbers, or an empty line to skip updates:3
✔ checking for file ‘/tmp/Rtmp77x4vi/remotesa26b5b965081/sqjin-CellChat-f0b2713/DESCRIPTION’ (596ms)
─ preparing ‘CellChat’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘CellChat_0.5.5.tar.gz’
Error: 25:1: unexpected symbol
24:
25: options
^
Execution halted
Error: Failed to install 'CellChat' from GitHub:
(converted from warning) installation of package ‘/tmp/Rtmp77x4vi/filea26bc952d13/CellChat_0.5.5.tar.gz’ had non-zero exit status
Then I tried to update "gdtools", but it failed again.
> devtools::install_github("sqjin/CellChat")
Downloading GitHub repo sqjin/CellChat@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: gdtools (0.2.2 -> 0.2.3) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1
gdtools (0.2.2 -> 0.2.3) [CRAN]
Skipping 3 packages not available: Biobase, BiocGenerics, ComplexHeatmap
Skipping 1 packages ahead of CRAN: cpp11
Installing 1 packages: gdtools
trying URL 'https://mirrors.tongji.edu.cn/CRAN/src/contrib/gdtools_0.2.3.tar.gz'
Content type 'application/octet-stream' length 33202 bytes (32 KB)
==================================================
downloaded 32 KB
Error: 25:1: unexpected symbol
24:
25: options
^
Execution halted
Error: Failed to install 'CellChat' from GitHub:
(converted from warning) installation of package ‘gdtools’ had non-zero exit status
Could you give any solution? Thanks in advance!
yancylau commented
There was something wrong with devtools. Finally I have make it by locally installing, but the *.so and *.o files in the src directory should be removed before installing .