Error issue while runnning GWAS

[faizalrezha]

Hi!

I am Rezha.

It is really nice to know your useful application. Unfortunately, I am encountering problem as follows:

1. The run was interrupted by an error.

2. Some packages seemed unistalled.

Could you please help me regarding these issues?

Thank you.

[Poissonfish]

Hello,

Would you try to individually install the missing packages?

[faizalrezha]

Hello,

I have tried but it still did not work. Maybe I did not do it with a correct way.

> install_github("multtest") Error in parse_repo_spec(repo) : Invalid git repo specification: 'multtest'

Would you mind to show me how to install them?

Thanks a lot.

[faizalrezha]

I somehow managed it to install but the error message "Error in contrib.url..." still appear.

I ran these command to install the packages individually.

`> BiocManager::install("LDheatmap", force = T)
'getOption("repos")' replaces
Bioconductor standard
repositories, see
'help("repositories", package
= "BiocManager")' for
details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19
(BiocManager 1.30.23), R
4.4.0 (2024-04-24 ucrt)
Installing package(s)
'LDheatmap'
Warning: package ‘LDheatmap’ is in use and will not be installed

BiocManager::install("multtest", force = T)
'getOption("repos")' replaces
Bioconductor standard
repositories, see
'help("repositories", package
= "BiocManager")' for
details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19
(BiocManager 1.30.23), R
4.4.0 (2024-04-24 ucrt)
Installing package(s)
'multtest'
trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/multtest_2.60.0.zip'
Content type 'application/zip' length 854175 bytes (834 KB)
downloaded 834 KB

package ‘multtest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Lenovo\AppData\Local\Temp\RtmpALkuAh\downloaded_packages

BiocManager::install("snpStats", force = T)
'getOption("repos")' replaces
Bioconductor standard
repositories, see
'help("repositories", package
= "BiocManager")' for
details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19
(BiocManager 1.30.23), R
4.4.0 (2024-04-24 ucrt)
Installing package(s)
'snpStats'
trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/snpStats_1.54.0.zip'
Content type 'application/zip' length 7884647 bytes (7.5 MB)
downloaded 7.5 MB

package ‘snpStats’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Lenovo\AppData\Local\Temp\RtmpALkuAh\downloaded_packages

source("http://zzlab.net/iPat/iPat_installation.r")
'getOption("repos")' replaces Bioconductor standard
repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0
(2024-04-24 ucrt)
'getOption("repos")' replaces Bioconductor standard
repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0
(2024-04-24 ucrt)
Skipping install of 'LDheatmap' from a github remote, the SHA1 (510c6005) has not changed since last install.
Use force = TRUE to force installation
Warning messages:
1: package(s) not installed when version(s) same as or greater
than current; use force = TRUE to re-install: 'multtest'
2: package(s) not installed when version(s) same as or greater
than current; use force = TRUE to re-install: 'snpStats'`

[faizalrezha]

Hello,

Is there anything I could do regarding this issue?

[Poissonfish]

It seems to me that you need to manually install "multtest" and "snpStats". They were not installed successfully according to the messages you provided

[faizalrezha]

Hi!

I am sorry for the late reply. I can just opened my progress recently.

I have already installed the missing packages snpStats and 'multtest' individually using command BiocManager::install("snpStats") as well as BiocManager::install("multtest").

And the console is shown below.
> BiocManager::install("snpStats") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14 ucrt) Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'snpStats'

> BiocManager::install("multtest") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14 ucrt) Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'multtest'

For the LDheatmap, I ran this command install_url('https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz') since the package is archived in CRAN.

The console appeared like this.

`> install_url('https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz')
Downloading package from url: https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz
Skipping 1 packages not available: snpStats
── R CMD build ──────────────────────────────
✔ checking for file 'C:\Users\Lenovo\AppData\Local\Temp\RtmpsH6qVZ\remotes6483ea94a63\LDheatmap/DESCRIPTION' (515ms)
─ preparing 'LDheatmap': (724ms)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
✔ checking vignette meta-information
─ checking for LF line-endings in source and make files and shell scripts (691ms)
─ checking for empty or unneeded directories
─ looking to see if a 'data/datalist' file should be added
─ building 'LDheatmap_1.0-6.tar.gz'

Installing package into ‘C:/Users/Lenovo/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)

• installing source package 'LDheatmap' ...
  ** using staged installation
  ** libs
  using C++ compiler: 'G__1.EXE (GCC) 13.2.0'
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-441.1/include" -DNDEBUG -I'C:/Users/Lenovo/AppData/Local/R/win-library/4.4/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GT_to_SnpMatrix.cpp -o GT_to_SnpMatrix.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-441.1/include" -DNDEBUG -I'C:/Users/Lenovo/AppData/Local/R/win-library/4.4/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++17 -shared -s -static-libgcc -o LDheatmap.dll tmp.def GT_to_SnpMatrix.o RcppExports.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA1/R/R-44~1.1/bin/x64 -lR
  installing to C:/Users/Lenovo/AppData/Local/R/win-library/4.4/00LOCK-LDheatmap/00new/LDheatmap/libs/x64
  ** R
  ** data
  ** demo
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  *** copying figures
  ** 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 (LDheatmap)`

However, when I ran the iPat again, the same error message was the same.