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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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installation and function #52

Closed HuiwuZhao closed 4 years ago

HuiwuZhao commented 4 years ago

BiocManager::install("uclouvain-cbio/depmap") failed

remotes::install_github("UCLouvain-CBIO/depmap", ref = "4a9f52ed6cf9c3821891ebdd9db317194d6518c9") can get 19Q1 release. How to get 19Q3

Also, depmap_copyNumber() function is not available

Thanks.

lgatto commented 4 years ago
HuiwuZhao commented 4 years ago

The sessionInfo was attached. I tried to install with the following codeslibrary(BiocManager)BiocManager::install("uclouvain-cbio/depmap") It was failed as shown in the attached file (installationfailure)

So I installed the package with the following code you posted remotes::install_github("UCLouvain-CBIO/depmap", ref = "4a9f52ed6cf9c3821891ebdd9db317194d6518c9") Though it only has the 19Q1 I had difficulty to install the development version.

Could you please help me out? Maybe you could send me the right ref for:  remotes::install_github("UCLouvain-CBIO/depmap", ref =?) Thanks. Huiwu Zhao 

On Thursday, March 5, 2020, 06:46:10 PM EST, Laurent Gatto <notifications@github.com> wrote:

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] stringr_1.4.0 tibble_2.1.3 viridis_0.5.1 viridisLite_0.3.0 ggplot2_3.2.1 gridExtra_2.3
[7] BiocStyle_2.12.0 depmap_0.99.3 dplyr_0.8.3 ExperimentHub_1.10.0 AnnotationHub_2.16.1 BiocFileCache_1.8.0 [13] dbplyr_1.4.2 BiocGenerics_0.30.0 BiocManager_1.30.9

loaded via a namespace (and not attached): [1] tidyselect_0.2.5 xfun_0.10 remotes_2.1.0 purrr_0.3.3
[5] colorspace_1.4-1 vctrs_0.2.0 htmltools_0.4.0 stats4_3.6.1
[9] yaml_2.2.0 utf8_1.1.4 interactiveDisplayBase_1.22.0 blob_1.2.0
[13] rlang_0.4.1 pillar_1.4.2 later_1.0.0 withr_2.1.2
[17] glue_1.3.1 DBI_1.0.0 rappdirs_0.3.1 bit64_0.9-7
[21] munsell_0.5.0 gtable_0.3.0 memoise_1.1.0 evaluate_0.14
[25] labeling_0.3 Biobase_2.44.0 knitr_1.25 IRanges_2.18.3
[29] fastmap_1.0.1 httpuv_1.5.2 curl_4.2 AnnotationDbi_1.46.1
[33] fansi_0.4.0 Rcpp_1.0.2 xtable_1.8-4 scales_1.0.0
[37] backports_1.1.5 promises_1.1.0 S4Vectors_0.22.1 mime_0.7
[41] bit_1.1-14 digest_0.6.22 stringi_1.4.3 shiny_1.4.0
[45] grid_3.6.1 cli_1.1.0 tools_3.6.1 magrittr_1.5
[49] lazyeval_0.2.2 RSQLite_2.1.2 crayon_1.3.4 pkgconfig_2.0.3
[53] zeallot_0.1.0 assertthat_0.2.1 rmarkdown_2.1 httr_1.4.1
[57] rstudioapi_0.10 R6_2.4.0 compiler_3.6.1

  • installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading help installing help indices converting help for package 'depmap' finding HTML links ... done RPPA html
    TPM html
    copyNumber html
    crispr html
    depmap html
    depmap_release html
    drug_sensitivity html
    metadata html
    mutationCalls html
    rnai html
     building package indices installing vignettes testing if installed package can be loaded from temporary location     arch - i386 snapshotDate(): 2019-04-29 snapshotDate(): 2019-04-29 Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: FUN(X[[i]], ...) error: 'rnai_19Q2' not found in ExperimentHub Error: loading failed Execution halted *** arch - x64 snapshotDate(): 2019-04-29 snapshotDate(): 2019-04-29 Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: FUN(X[[i]], ...) error: 'rnai_19Q2' not found in ExperimentHub Error: loading failed Execution halted ERROR: loading failed for 'i386', 'x64'
  • removing 'C:/R-3.6.1/library/depmap'
  • restoring previous 'C:/R-3.6.1/library/depmap' Error: Failed to install 'depmap' from GitHub: (converted from warning) installation of package ‘C:/Users/hzhao21/AppData/Local/Temp/1/RtmpwDpqoO/file34b832834f1e/depmap_1.1.2.tar.gz’ had non-zero exit status
tfkillian commented 4 years ago

@HuiwuZhao - I have been able to install the latest version of the depmap (v 1.1.2) successfully without issues using BiocManager::install("uclouvain-cbio/depmap") Additionally, the depmap_copyNumber function also works correctly.

I suggest that you update your R to the latest version 3.6.3, and update the AnnotationHub and ExperimentHub packages to the latest versions. You are running AnnotationHub_2.16.1 and depmap requires the latest version of ExperimentHub to access the data. (ExperimentHub fully depends on AnnotationHub(>= 2.17.9) to function properly). Also, I do not see BiocVersion installed in your sessionInfo. I suggest installing the latest version of that as well: BiocManager::install("BiocVersion")

You can see my sessionInfo and depmap_copyNumber output below:

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_BE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_BE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_BE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_BE.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] depmap_1.1.2 dplyr_0.8.5

loaded via a namespace (and not attached): [1] tidyselect_1.0.0 remotes_2.1.1 BiocVersion_3.10.1
[4] purrr_0.3.3 vctrs_0.2.3 htmltools_0.4.0
[7] stats4_3.6.3 BiocFileCache_1.10.2 yaml_2.2.1
[10] interactiveDisplayBase_1.24.0 blob_1.2.1 rlang_0.4.5
[13] pkgbuild_1.0.6 pillar_1.4.3 later_1.0.0
[16] glue_1.3.2 withr_2.1.2 DBI_1.1.0
[19] rappdirs_0.3.1 BiocGenerics_0.32.0 bit64_0.9-7
[22] dbplyr_1.4.2 ExperimentHub_1.12.0 memoise_1.1.0
[25] Biobase_2.46.0 IRanges_2.20.2 callr_3.4.2
[28] fastmap_1.0.1 httpuv_1.5.2 ps_1.3.2
[31] parallel_3.6.3 curl_4.3 fansi_0.4.1
[34] AnnotationDbi_1.48.0 Rcpp_1.0.3 xtable_1.8-4
[37] backports_1.1.5 promises_1.1.0 BiocManager_1.30.10
[40] S4Vectors_0.24.3 mime_0.9 bit_1.1-15.2
[43] AnnotationHub_2.18.0 digest_0.6.25 processx_3.4.2
[46] shiny_1.4.0 rprojroot_1.3-2 cli_2.0.2
[49] tools_3.6.3 magrittr_1.5 tibble_2.1.3
[52] RSQLite_2.2.0 crayon_1.3.4 pkgconfig_2.0.3
[55] prettyunits_1.1.1 assertthat_0.2.1 httr_1.4.1
[58] rstudioapi_0.11 R6_2.4.1 compiler_3.6.3

depmap_copyNumber() snapshotDate(): 2019-10-22 see ?depmap and browseVignettes('depmap') for documentation loading from cache A tibble: 2,708,508 x 4 depmap_id cell_line compound dependency

1 ACH-000001 NIHOVCAR3_OVARY BRD-A00077618-236-07-6::2.5::HTS -0.0156 2 ACH-000007 LS513_LARGE_INTESTINE BRD-A00077618-236-07-6::2.5::HTS -0.0957 3 ACH-000008 A101D_SKIN BRD-A00077618-236-07-6::2.5::HTS 0.379 4 ACH-000010 NCIH2077_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.119 5 ACH-000011 253J_URINARY_TRACT BRD-A00077618-236-07-6::2.5::HTS 0.145 6 ACH-000012 HCC827_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.103 7 ACH-000013 ONCODG1_OVARY BRD-A00077618-236-07-6::2.5::HTS 0.353 8 ACH-000014 HS294T_SKIN BRD-A00077618-236-07-6::2.5::HTS 0.128 9 ACH-000015 NCIH1581_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.167 10 ACH-000018 T24_URINARY_TRACT BRD-A00077618-236-07-6::2.5::HTS 0.832 … with 2,708,498 more rows
HuiwuZhao commented 4 years ago

I update my R to  the latest version 3.6.3 and use AnnotationHub_2.18.0. When I tried to install "depmap". It gave "no internet connection" error as shown below, though I am online. Any idea how to fix it? Thanks. Huiwu

library(BiocManager)> BiocManager::install("uclouvain-cbio/depmap") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)Installing github package(s) 'uclouvain-cbio/depmap'Downloading GitHub repo uclouvain-cbio/depmap@masterThese 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: dplyr (0.8.4 -> 0.8.5) [CRAN]5: vctrs (0.2.3 -> 0.2.4) [CRAN] Enter one or more numbers, or an empty line to skip updates:1dplyr (0.8.4 -> 0.8.5) [CRAN]vctrs (0.2.3 -> 0.2.4) [CRAN]Installing 2 packages: dplyr, vctrs   There are binary versions available but the source versions are later:      binary source needs_compilationdplyr  0.8.4  0.8.5              TRUEvctrs  0.2.3  0.2.4              TRUE   Binaries will be installedtrying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/dplyr_0.8.4.zip'Content type 'application/zip' length 3221142 bytes (3.1 MB)downloaded 3.1 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/vctrs_0.2.3.zip'Content type 'application/zip' length 986125 bytes (963 KB)downloaded 963 KB package ‘dplyr’ successfully unpacked and MD5 sums checkedpackage ‘vctrs’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hzhao21\AppData\Local\Temp\1\RtmpMDCYoh\downloaded_packagesRunning R CMD build... checking for file 'C:\Users\hzhao21\AppData\Local\Temp\1\RtmpMDCYoh\remotes154c4e8d2cc6\UCLouvain-CBIO-depmap-7dad94f/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_1.1.2.tar.gz' installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading help installing help indices  converting help for package 'depmap'    finding HTML links ... done    RPPA                                    html      TPM                                     html      copyNumber                              html      crispr                                  html      depmap                                  html      depmap_release                          html      drug_sensitivity                        html      metadata                                html      mutationCalls                           html      rnai                                    html   building package indices installing vignettes testing if installed package can be loaded from temporary location** arch - i386No internet connection using 'localHub=TRUE'snapshotDate(): 2020-03-09Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details:  call: FUN(X[[i]], ...)  error: 'metadata_19Q1' not found in ExperimentHubError: loading failedExecution halted arch - x64No internet connection using 'localHub=TRUE'snapshotDate(): 2020-03-09Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details:  call: FUN(X[[i]], ...)  error: 'metadata_19Q1' not found in ExperimentHubError: loading failedExecution haltedERROR: loading failed for 'i386', 'x64'* removing 'C:/R-3.6.3/library/depmap'Error: Failed to install 'depmap' from GitHub:  (converted from warning) installation of package ‘C:/Users/hzhao21/AppData/Local/Temp/1/RtmpMDCYoh/file154c2ec5462d/depmap_1.1.2.tar.gz’ had non-zero exit status> sessionInfo()R version 3.6.3 (2020-02-29)Platform: x86_64-w64-mingw32/x64 (64-bit)Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252     attached base packages:[1] stats     graphics  grDevices utils     datasets  methods   base      other attached packages:[1] BiocManager_1.30.10 loaded via a namespace (and not attached):[1] compiler_3.6.3 tools_3.6.3    curl_4.3       remotes_2.1.1 

Huiwu Zhao 

On Tuesday, March 10, 2020, 05:24:11 AM EDT, T F Killian <notifications@github.com> wrote:

HuiwiZhao, I have able to install the latest version of the depmap (v 1.1.2) successfully without issues, and the depmap_copyNumber function also works correctly.

I suggest that you update your R to the latest version 3.6.3, and update the AnnotationHub and ExperimentHub packages to the latest versions. You are running AnnotationHub_2.16.1 and depmap requires the latest version of ExperimentHub to access the data. (ExperimentHub fully depends on AnnotationHub(>= 2.17.9) to function properly). Also, I do not see BiocVersion installed in your sessionInfo. I suggest installing the latest version of that as well: BiocManager::install("BiocVersion")

You can see my sessionInfo and depmap_copyNumber output below:

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_BE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_BE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_BE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_BE.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] depmap_1.1.2 dplyr_0.8.5

loaded via a namespace (and not attached): [1] tidyselect_1.0.0 remotes_2.1.1 BiocVersion_3.10.1 [4] purrr_0.3.3 vctrs_0.2.3 htmltools_0.4.0 [7] stats4_3.6.3 BiocFileCache_1.10.2 yaml_2.2.1 [10] interactiveDisplayBase_1.24.0 blob_1.2.1 rlang_0.4.5 [13] pkgbuild_1.0.6 pillar_1.4.3 later_1.0.0 [16] glue_1.3.2 withr_2.1.2 DBI_1.1.0 [19] rappdirs_0.3.1 BiocGenerics_0.32.0 bit64_0.9-7 [22] dbplyr_1.4.2 ExperimentHub_1.12.0 memoise_1.1.0 [25] Biobase_2.46.0 IRanges_2.20.2 callr_3.4.2 [28] fastmap_1.0.1 httpuv_1.5.2 ps_1.3.2 [31] parallel_3.6.3 curl_4.3 fansi_0.4.1 [34] AnnotationDbi_1.48.0 Rcpp_1.0.3 xtable_1.8-4 [37] backports_1.1.5 promises_1.1.0 BiocManager_1.30.10 [40] S4Vectors_0.24.3 mime_0.9 bit_1.1-15.2 [43] AnnotationHub_2.18.0 digest_0.6.25 processx_3.4.2 [46] shiny_1.4.0 rprojroot_1.3-2 cli_2.0.2 [49] tools_3.6.3 magrittr_1.5 tibble_2.1.3 [52] RSQLite_2.2.0 crayon_1.3.4 pkgconfig_2.0.3 [55] prettyunits_1.1.1 assertthat_0.2.1 httr_1.4.1 [58] rstudioapi_0.11 R6_2.4.1 compiler_3.6.3

depmap_copyNumber() snapshotDate(): 2019-10-22 see ?depmap and browseVignettes('depmap') for documentation loading from cache

A tibble: 2,708,508 x 4

depmap_id cell_line compound dependency

1 ACH-000001 NIHOVCAR3_OVARY BRD-A00077618-236-07-6::2.5::HTS -0.0156 2 ACH-000007 LS513_LARGE_INTESTINE BRD-A00077618-236-07-6::2.5::HTS -0.0957 3 ACH-000008 A101D_SKIN BRD-A00077618-236-07-6::2.5::HTS 0.379 4 ACH-000010 NCIH2077_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.119 5 ACH-000011 253J_URINARY_TRACT BRD-A00077618-236-07-6::2.5::HTS 0.145 6 ACH-000012 HCC827_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.103 7 ACH-000013 ONCODG1_OVARY BRD-A00077618-236-07-6::2.5::HTS 0.353 8 ACH-000014 HS294T_SKIN BRD-A00077618-236-07-6::2.5::HTS 0.128 9 ACH-000015 NCIH1581_LUNG BRD-A00077618-236-07-6::2.5::HTS 0.167 10 ACH-000018 T24_URINARY_TRACT BRD-A00077618-236-07-6::2.5::HTS 0.832

… with 2,708,498 more rows

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lgatto commented 4 years ago

@HuiwuZhao - could you please format your messages properly.

tfkillian commented 4 years ago

@HuiwuZhao - it appears that the error you are experiencing is likely related to AnnotationHub not able to connect to the localHub. See: https://rdrr.io/bioc/AnnotationHub/src/R/AnnotationHub-class.R

In this case, I would suggest making a post on the Bioconductor Support Site: https://support.bioconductor.org/

You may also look on the AnnotationHub github and search for similar issues or create one: https://github.com/Bioconductor/AnnotationHub/issues/5

Lastly, have you updated all packages your environment, like so: BiocManager::install()

After you have done so, could you post a formatted sessionInfo if the error persists?

HuiwuZhao commented 4 years ago

Thanks. Once I use the version 3.6.3 of R. I am not able to connect with the AnnotationHub and could not find a solution. Once I switched back to 3.6.1, AnnotationHub is fine now, though DepMap asked for 3.6.3. I guess I am not able to figure out the way to use the DepMap at this moment.  

Thanks. Huiwu Zhao

lgatto commented 4 years ago

Bioconductor has two version, release and development. The version of depmap here on github is the latest development version, hence the possible requirement for the latest R. It is however possible to install it with R 3.6.2, as shown below:

> version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          6.2                         
year           2019                        
month          12                          
day            12                          
svn rev        77560                       
language       R                           
version.string R version 3.6.2 (2019-12-12)
nickname       Dark and Stormy Night       
> library(AnnotationHub)
> BiocManager::install("UCLouvain-CBIO/depmap")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing github package(s) 'UCLouvain-CBIO/depmap'
Downloading GitHub repo UCLouvain-CBIO/depmap@master
✔  checking for file ‘/tmp/RtmpIYy6Wn/remotes56553b2d5825/UCLouvain-CBIO-depmap-7dad94f/DESCRIPTION’ (442ms)
─  preparing ‘depmap’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘depmap_1.1.2.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
snapshotDate(): 2019-10-22
snapshotDate(): 2019-10-22
snapshotDate(): 2019-10-22
** testing if installed package can be loaded from final location
snapshotDate(): 2019-10-22
snapshotDate(): 2019-10-22
snapshotDate(): 2019-10-22
** testing if installed package keeps a record of temporary installation path
* DONE (depmap)