为什么不能成功安装

[kly-plap]

1: All
2: CRAN packages only
3: None
4: rlang (1.1.5 -> 1.1.6 ) [CRAN]
5: curl (6.2.2 -> 6.2.3 ) [CRAN]
6: cli (3.6.4 -> 3.6.5 ) [CRAN]
7: stringi (1.8.4 -> 1.8.7 ) [CRAN]
8: data.table (1.17.0 -> 1.17.4) [CRAN]

为什么用这个命令安装不上。if(!require("remotes")) install.packages("remotes")
remotes::install_github("RajLabMSSM/echolocatoR")
library(echolocatoR)
usethis::create_github_token() # 创建 GitHub token
gitcreds::gitcreds_set() # 设置 token

Enter one or more numbers, or an empty line to skip updates: 3
Downloading GitHub repo neurogenomics/MungeSumstats@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: rlang (1.1.5 -> 1.1.6 ) [CRAN]
5: curl (6.2.2 -> 6.2.3 ) [CRAN]
6: cli (3.6.4 -> 3.6.5 ) [CRAN]
7: stringi (1.8.4 -> 1.8.7 ) [CRAN]
8: data.table (1.17.0 -> 1.17.4) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ──────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\空空\AppData\Local\Temp\RtmpqeJzGL\remotes816c54c374f\neurogenomics-MungeSumstats-f1ce571/DESCRIPTION' (366ms)
─ preparing 'MungeSumstats': (480ms)
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (459ms)
─ checking for empty or unneeded directories
─ looking to see if a 'data/datalist' file should be added
─ building 'MungeSumstats_1.13.4.tar.gz'

将程序包安装入‘C:/Users/空空/AppData/Local/R/win-library/4.4’
(因为‘lib’没有被指定)
ERROR: dependencies 'GenomicRanges', 'IRanges', 'GenomeInfoDb', 'BSgenome', 'Biostrings', 'VariantAnnotation', 'rtracklayer' are not available for package 'MungeSumstats'

• removing 'C:/Users/空空/AppData/Local/R/win-library/4.4/MungeSumstats'
  Downloading GitHub repo neurogenomics/MungeSumstats@HEAD
  Skipping MungeSumstats, it is already being installed
  ── R CMD build ──────────────────────────────────────────────────────────────────────────
  ✔ checking for file 'C:\Users\空空\AppData\Local\Temp\RtmpqeJzGL\remotes816c45d07848\RajLabMSSM-echodata-0d19cc1/DESCRIPTION' (336ms)
  ─ preparing 'echodata':
  ✔ checking DESCRIPTION meta-information ...
  ─ checking for LF line-endings in source and make files and shell scripts (365ms)
  ─ checking for empty or unneeded directories
  ─ building 'echodata_0.99.17.tar.gz'

将程序包安装入‘C:/Users/空空/AppData/Local/R/win-library/4.4’
(因为‘lib’没有被指定)
ERROR: dependency 'MungeSumstats' is not available for package 'echodata'

• removing 'C:/Users/空空/AppData/Local/R/win-library/4.4/echodata'
  Downloading GitHub repo RajLabMSSM/echodata@HEAD
  Skipping echodata, it is already being installed
  ── R CMD build ──────────────────────────────────────────────────────────────────────────
  ✔ checking for file 'C:\Users\空空\AppData\Local\Temp\RtmpqeJzGL\remotes816c102f769d\RajLabMSSM-echoconda-671f5e0/DESCRIPTION' (350ms)
  ─ preparing 'echoconda':
  ✔ checking DESCRIPTION meta-information ...
  ─ checking for LF line-endings in source and make files and shell scripts
  ─ checking for empty or unneeded directories
  Omitted 'LazyData' from DESCRIPTION
  ─ building 'echoconda_0.99.10.tar.gz'
  Warning: file 'echoconda/configure' did not have execute permissions: corrected

将程序包安装入‘C:/Users/空空/AppData/Local/R/win-library/4.4’
(因为‘lib’没有被指定)
ERROR: dependencies 'basilisk', 'basilisk.utils', 'echodata' are not available for package 'echoconda'

• removing 'C:/Users/空空/AppData/Local/R/win-library/4.4/echoconda'
  Downloading GitHub repo RajLabMSSM/downloadR@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: rlang (1.1.5 -> 1.1.6 ) [CRAN]
5: cli (3.6.4 -> 3.6.5 ) [CRAN]
6: curl (6.2.2 -> 6.2.3 ) [CRAN]
7: data.table (1.17.0 -> 1.17.4) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
Downloading GitHub repo RajLabMSSM/echoconda@HEAD
Skipping echoconda, it is already being installed
Downloading GitHub repo RajLabMSSM/echoconda@HEAD
Skipping echoconda, it is already being installed
── R CMD build ──────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\空空\AppData\Local\Temp\RtmpqeJzGL\remotes816c58115a35\RajLabMSSM-downloadR-39d7b0d/DESCRIPTION' (344ms)
─ preparing 'downloadR':
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building 'downloadR_0.99.7.tar.gz'

将程序包安装入‘C:/Users/空空/AppData/Local/R/win-library/4.4’
(因为‘lib’没有被指定)
ERROR: dependency 'echoconda' is not available for package 'downloadR'

• removing 'C:/Users/空空/AppData/Local/R/win-library/4.4/downloadR'
  Downloading GitHub repo RajLabMSSM/echodata@HEAD
  Skipping echodata, it is already being installed
  Downloading GitHub repo RajLabMSSM/echotabix@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: rlang (1.1.5 -> 1.1.6 ) [CRAN]
5: cli (3.6.4 -> 3.6.5 ) [CRAN]
6: data.table (1.17.0 -> 1.17.4) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
错误: Failed to install 'unknown package' from GitHub:
Failed to install 'unknown package' from GitHub:
Failed to install 'unknown package' from GitHub:
HTTP error 403.
API rate limit exceeded for 112.96.228.183. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

Rate limit remaining: 0/60
Rate limit reset at: 2025-05-28 16:20:39 UTC

To increase your GitHub API rate limit

• Use usethis::create_github_token() to create a Personal Access Token.
• Use gitcreds::gitcreds_set() to add the token.
  此外: 警告信息:
  1: In i.p(...) :
  安装程序包‘C:/Users/空空/AppData/Local/Temp/RtmpqeJzGL/file816c50145fba/MungeSumstats_1.13.4.tar.gz’时退出狀態的值不是0
  2: In i.p(...) :
  安装程序包‘C:/Users/空空/AppData/Local/Temp/RtmpqeJzGL/file816c6f575f49/echodata_0.99.17.tar.gz’时退出狀態的值不是0
  3: In i.p(...) :
  安装程序包‘C:/Users/空空/AppData/Local/Temp/RtmpqeJzGL/file816c22781d33/echoconda_0.99.10.tar.gz’时退出狀態的值不是0
  4: In i.p(...) :
  安装程序包‘C:/Users/空空/AppData/Local/Temp/RtmpqeJzGL/file816c5f341445/downloadR_0.99.7.tar.gz’时退出狀態的值不是0

[bschilder]

Try:

if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("RajLabMSSM/echolocatoR")
library(echolocatoR)

[kly-plap]

if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("RajLabMSSM/echolocatoR")
library(echolocatoR)，使用这个命令安装还是报错。
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘DelayedArray’ failed
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Arrays_1.2.1.tar.gz'
Content type 'application/gzip' length 282089 bytes (275 KB)

downloaded 275 KB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biobase_2.62.0.tar.gz'
Content type 'application/gzip' length 1795862 bytes (1.7 MB)

downloaded 526 KB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biobase_2.62.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/src/contrib/Biobase_2.62.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘Biobase’ failed
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Rhtslib_2.4.1.tar.gz'
Content type 'application/gzip' length 4581411 bytes (4.4 MB)

downloaded 174 KB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Rhtslib_2.4.1.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/src/contrib/Rhtslib_2.4.1.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘Rhtslib’ failed
trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz'
Content type 'application/gzip' length 12284235 bytes (11.7 MB)

downloaded 240 KB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘GenomeInfoDbData’ failed
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz'
Content type 'application/gzip' length 67825 bytes (66 KB)

downloaded 66 KB