installation errors. - Githubissues

Travis13197 commented 1 year ago

install_github("UCLouvain-CBIO/depmap")

info: Warning: package 'dplyr' was built under R version 4.2.3 Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-04-11 Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: FUN(X[[i]], ...) error: 'crispr_22Q1' not found in ExperimentHub Error: loading failed Execution halted ERROR: loading failed

i don't know how to fix this. please help

Travis13197 commented 1 year ago

install_github("UCLouvain-CBIO/depmap") BiocManager::install("depmap",version = "3.16") remotes::install_github("UCLouvain-CBIO/depmap", ref ="4a9f52ed6cf9c3821891ebdd9db317194d6518c9")

those methods can't help either.

lgatto commented 1 year ago

Could you please provide the complete inputs and outputs and your session information (with sessionInfo()).

Also, do not install from Github, this is likely to fail, only use BiocManager::install("depmap") (without setting the version). If you need a more recent version of depmap, you will need to have a recent version of R.

Travis13197 commented 1 year ago

Thanks! Here is session info: R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] enrichplot_1.18.4 DOSE_3.24.2 org.Mm.eg.db_3.16.0 AnnotationDbi_1.60.2 Biobase_2.58.0 clusterProfiler_4.6.2 [7] ggfortify_0.4.16 data.table_1.14.8 ggpubr_0.6.0 rtracklayer_1.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[13] IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.44.0 stringr_1.5.0 dplyr_1.1.1 tidyr_1.3.0
[19] msigdbr_7.5.1 ggplot2_3.4.2

loaded via a namespace (and not attached): [1] ggtree_3.6.2 fgsea_1.24.0 colorspace_2.1-0 gson_0.1.0 ggsignif_0.6.4
[6] rjson_0.2.21 qvalue_2.30.0 XVector_0.38.0 aplot_0.1.10 rstudioapi_0.14
[11] farver_2.1.1 remotes_2.4.2 graphlayouts_0.8.4 ggrepel_0.9.3 bit64_4.0.5
[16] scatterpie_0.1.8 fansi_1.0.4 codetools_0.2-19 splines_4.2.2 cachem_1.0.7
[21] GOSemSim_2.24.0 polyclip_1.10-4 jsonlite_1.8.4 Rsamtools_2.14.0 broom_1.0.4
[26] GO.db_3.16.0 png_0.1-8 ggforce_0.4.1 BiocManager_1.30.20 compiler_4.2.2
[31] httr_1.4.5 backports_1.4.1 lazyeval_0.2.2 Matrix_1.5-4 fastmap_1.1.1
[36] cli_3.6.1 tweenr_2.0.2 tools_4.2.2 igraph_1.4.2 gtable_0.3.3
[41] glue_1.6.2 GenomeInfoDbData_1.2.9 reshape2_1.4.4 fastmatch_1.1-3 Rcpp_1.0.10
[46] carData_3.0-5 vctrs_0.6.1 Biostrings_2.66.0 nlme_3.1-162 ape_5.7-1
[51] babelgene_22.9 ggraph_2.1.0 MeSHDbi_1.34.0 lifecycle_1.0.3 restfulr_0.0.15
[56] rstatix_0.7.2 XML_3.99-0.14 zlibbioc_1.44.0 MASS_7.3-58.3 scales_1.2.1
[61] tidygraph_1.2.3 vroom_1.6.1 MatrixGenerics_1.10.0 parallel_4.2.2 SummarizedExperiment_1.28.0 [66] RColorBrewer_1.1-3 yaml_2.3.7 memoise_2.0.1 gridExtra_2.3 downloader_0.4
[71] ggfun_0.0.9 HDO.db_0.99.1 yulab.utils_0.0.6 stringi_1.7.12 RSQLite_2.3.0
[76] BiocIO_1.8.0 tidytree_0.4.2 BiocParallel_1.32.6 rlang_1.1.0 pkgconfig_2.0.3
[81] matrixStats_0.63.0 bitops_1.0-7 lattice_0.21-8 purrr_1.0.1 treeio_1.22.0
[86] patchwork_1.1.2 GenomicAlignments_1.34.1 shadowtext_0.1.2 cowplot_1.1.1 bit_4.0.5
[91] tidyselect_1.2.0 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[96] DelayedArray_0.23.2 DBI_1.1.3 pillar_1.9.0 withr_2.5.0 KEGGREST_1.38.0
[101] abind_1.4-5 RCurl_1.98-1.12 tibble_3.2.1 crayon_1.5.2 car_3.1-2
[106] utf8_1.2.3 tzdb_0.3.0 viridis_0.6.2 grid_4.2.2 blob_1.2.4
[111] digest_0.6.31 gridGraphics_0.5-1 munsell_0.5.0 viridisLite_0.4.1 ggplotify_0.1.0

When I use BiocManager::install("depmap") And The same error occurred: Warning: package 'dplyr' was built under R version 4.2.3 Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-04-11 Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: FUN(X[[i]], ...) error: 'crispr_22Q1' not found in ExperimentHub Error: loading failed Execution halted ERROR: loading failed

lgatto commented 1 year ago

This is weird:

Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
Using 'localHub=TRUE'

are you on-line when running the code? Make sure you are, then do the following:

BiocManager::install("ExperimentHub")
library(ExperimentHub)
eh <- ExperimentHub()
query(eh, "crispr_2")

What do you get?

Travis13197 commented 1 year ago

library(ExperimentHub) eh <- ExperimentHub()


|===================================================================================================================================================| 100%
snapshotDate(): 2022-10-31
query(eh, "crispr_2")
ExperimentHub with 10 records
# snapshotDate(): 2022-10-31
# $dataprovider: Broad Institute
# $species: Homo sapiens
# $rdataclass: tibble
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, rdatapath,
#   sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH3290"]]'

       title

it seemed that crispr_22Q1 was downloaded. 

**but after running above codes, i re-ran **
`BiocManager::install("depmap")`
same errors occurred:

Warning: package 'dplyr' was built under R version 4.2.3 Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-04-12 Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: FUN(X[[i]], ...) error: 'crispr_22Q1' not found in ExperimentHub Error: loading failed Execution halted ERROR: loading failed



it seems like a network problem(can not connect to ExperimentHub server), however it is quite strange that when i ran `eh <- ExperimentHub()`: it could download related data.

lgatto commented 1 year ago

You are not showing everything - there's more code after typing BiocManager::install("depmap"):

> BiocManager::install("depmap")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-02
  r83238)
Installing package(s) 'depmap'
trying URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.12.0.tar.gz'
Content type 'application/x-gzip' length 1382308 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘depmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-10-31
** testing if installed package can be loaded from final location
snapshotDate(): 2022-10-31
** testing if installed package keeps a record of temporary installation path
* DONE (depmap)

Is you issue happening after the ** testing if installed package can be loaded from temporary location?

Are you sure you don't have intermittent network issues?

Travis13197 commented 1 year ago

> BiocManager::install("depmap")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://mirror.lzu.edu.cn/CRAN/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'depmap'
安装源码包‘depmap’

trying URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.12.0.tar.gz'
Content type 'application/x-gzip' length 1382308 bytes (1.3 MB)
downloaded 1.3 MB

* installing *source* package 'depmap' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'dplyr' was built under R version 4.2.3 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'dplyr' was built under R version 4.2.3
Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
snapshotDate(): 2023-04-12
Error: package or namespace load failed for 'depmap':
 .onLoad failed in loadNamespace() for 'depmap', details:
  call: FUN(X[[i]], ...)
  error: 'crispr_22Q1' not found in ExperimentHub
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/kkk/AppData/Local/R/win-library/4.2/depmap'

下载的程序包在
    ‘C:\Users\kkk\AppData\Local\Temp\Rtmp8Sm0vd\downloaded_packages’里
Old packages: 'DelayedArray', 'git2r', 'leidenbase', 'pec', 'RSQLite', 'lattice', 'Matrix'

lgatto commented 1 year ago

I can reproduce your error if I close the wifi right after the package has downloaded, i.e at installing *source* package 'depmap' .... Do you have any reasons to believe that there are some network restrictions on your computer?

I would suggest you ask you question on the Bioconductor form, so gather wider input on this issue.

0106WeiWeiDeng commented 8 months ago

Try :

download package from bioconductor website: depmap_1.15.0.tar.gz
in terminal: R CMD INSTALL depmap_1.15.0.tar.gz

soleded commented 8 months ago

I have the similar question, and don't know how to solve this problem

BiocManager::install("uclouvain-cbio/depmap") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://mirror-hk.koddos.net/CRAN/ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16 ucrt) Installing github package(s) 'uclouvain-cbio/depmap' Downloading GitHub repo uclouvain-cbio/depmap@HEAD Running R CMD build...

checking for file 'C:\Users\SOLEDED\AppData\Local\Temp\RtmpYTP78I\remotes49a426b768b8\UCLouvain-CBIO-depmap-f716330/DESCRIPTION' ... OK

preparing 'depmap':

checking DESCRIPTION meta-information ... OK

checking for LF line-endings in source and make files and shell scripts

checking for empty or unneeded directories

building 'depmap_1.11.2.tar.gz'

installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: (function (cond) error: error in evaluating the argument 'x' in selecting a method for function 'query': Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? Error: loading failed Execution halted ERROR: loading failed

removing 'C:/Users/SOLEDED/AppData/Local/R/win-library/4.3/depmap' Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.3.1/library packages: foreign, KernSmooth, lattice, Matrix, mgcv, nlme, rpart, spatial, survival Warning message: In i.p(...) : 安装程序包‘C:/Users/SOLEDED/AppData/Local/Temp/RtmpYTP78I/file49a46d152fd1/depmap_1.11.2.tar.gz’时退出狀態的值不是0

lgatto commented 8 months ago

This is a different issue - see here (if you are on the Bioconductor slack).

In a nutshell:

wait 24 hours, update BiocFileCache, et try again
if you can wait, BiocManager::install("Bioconductor/BiocFileCache")

and try again

YanlanSun commented 6 months ago

I also face the similar problem, can you give me sone suggestions? Thank you very much! BiocManager::install("depmap") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31 ucrt) Installing package(s) 'depmap' 安装源码包‘depmap’

试开URL’https://bioconductor.org/packages/3.18/data/experiment/src/contrib/depmap_1.16.0.tar.gz' Content type 'application/x-gzip' length 1409559 bytes (1.3 MB) downloaded 1.3 MB

installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: h(simpleError(msg, call)) error: error in evaluating the argument 'x' in selecting a method for function 'query': Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' Error: loading failed Execution halted ERROR: loading failed
removing 'D:/R/R-4.3.2/library/depmap'

下载的程序包在 ‘C:\Users\18817\AppData\Local\Temp\RtmpSyRljJ\downloaded_packages’里 Old packages: 'mgcv' Update all/some/none? [a/s/n]: a

有二进制版本的，但源代码版本是后来的: binary source needs_compilation mgcv 1.9-0 1.9-1 TRUE

Binaries will be installed 试开URL’https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.3/mgcv_1.9-0.zip' Content type 'application/zip' length 3389936 bytes (3.2 MB) downloaded 3.2 MB

程序包‘mgcv’打开成功，MD5和检查也通过

下载的二进制程序包在 C:\Users\18817\AppData\Local\Temp\RtmpSyRljJ\downloaded_packages里 Warning message: In install.packages(...) : 安装程序包‘depmap’时退出狀態的值不是0

YanlanSun commented 6 months ago

I want to install MAGeCKFlute, but the dependency "depmap" is not available, can I slove this problem through

wait 24 hours, update BiocFileCache, et try again if you can wait, BiocManager::install("Bioconductor/BiocFileCache") and try again

I am confused why I have to wait 24h and waiting 24h before or after BiocManager::install("Bioconductor/BiocFileCache") Thank you very much!

devtools::install_github("liulab-dfci/MAGeCKFlute") Downloading GitHub repo liulab-dfci/MAGeCKFlute@HEAD Installing 1 packages: depmap 安装源码包‘depmap’

试开URL’https://bioconductor.org/packages/3.18/data/experiment/src/contrib/depmap_1.16.0.tar.gz' Content type 'application/x-gzip' length 1409559 bytes (1.3 MB) downloaded 1.3 MB

installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: h(simpleError(msg, call)) error: error in evaluating the argument 'x' in selecting a method for function 'query': Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' Error: loading failed Execution halted ERROR: loading failed
removing 'D:/R/R-4.3.2/library/depmap'

下载的程序包在 ‘C:\Users\18817\AppData\Local\Temp\RtmpkBpBQZ\downloaded_packages’里 ── R CMD build ────────────────────────────────────────────────────────────────── ✔ checking for file 'C:\Users\18817\AppData\Local\Temp\RtmpkBpBQZ\remotes5b823a16ed4\liulab-dfci-MAGeCKFlute-20a356c/DESCRIPTION' ─ preparing 'MAGeCKFlute': (965ms) ✔ 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 'MAGeCKFlute_1.99.0.tar.gz'

ERROR: dependency 'depmap' is not available for package 'MAGeCKFlute'

removing 'D:/R/R-4.3.2/library/MAGeCKFlute' Warning messages: 1: In i.p(...) : 安装程序包‘depmap’时退出狀態的值不是0 2: In i.p(...) : 安装程序包‘C:/Users/18817/AppData/Local/Temp/RtmpkBpBQZ/file5b855db384f/MAGeCKFlute_1.99.0.tar.gz’时退出狀態的值不是0

lgatto commented 6 months ago

Try to load ExperimentHub, to create the cache and/or see the instructions in the error message.

YanlanSun commented 6 months ago

when I try to load ExperimentHub, it still indicates connecting unsuccessfully, what I can do?

lgatto commented 6 months ago

Have you tried following the instructions?

Otherwise, please ask on https://support.bioconductor.org/

UCLouvain-CBIO / depmap

installation errors. #85