Load library ampvis2 error

[Jessie-HOU]

Hi there!

I have successfully installed ampvi2 package and used it once normally. But when I load this ampvis2 package into R this time, it threw out the following error:

library(ampvis2) Error: package or namespace load failed for ‘ampvis2’: .onAttach failed in attachNamespace() for 'ampvis2', details: call: fun(libname, pkgname) error: object 'remote_version' not found In addition: Warning message: In file(con, "r") : URL 'https://raw.githubusercontent.com/madsalbertsen/ampvis2/master/DESCRIPTION': status was 'Couldn't connect to server'

The Rstudio basic information is:

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] tidyr_1.0.2 ape_5.2 dplyr_0.8.5 vegan_2.5-2 lattice_0.20-35 [6] permute_0.9-4 ggplot2_3.3.0 reshape2_1.4.4

loaded via a namespace (and not attached): [1] ggrepel_0.8.0 Rcpp_1.0.4 lubridate_1.7.4 assertthat_0.2.0
[5] digest_0.6.18 foreach_1.4.4 cellranger_1.1.0 R6_2.3.0
[9] plyr_1.8.4 httr_1.4.1 pillar_1.4.3 rlang_0.4.5
[13] lazyeval_0.2.1 readxl_1.3.1 rstudioapi_0.11 data.table_1.11.8 [17] Matrix_1.2-14 labeling_0.3 stringr_1.4.0 htmlwidgets_1.5.1 [21] munsell_0.5.0 compiler_3.5.1 pkgconfig_2.0.2 mgcv_1.8-24
[25] htmltools_0.3.6 biomformat_1.8.0 tidyselect_0.2.5 tibble_2.1.3
[29] ampvis2_2.5.9 codetools_0.2-15 fansi_0.4.0 viridisLite_0.3.0 [33] crayon_1.3.4 withr_2.1.2 MASS_7.3-51 grid_3.5.1
[37] ggnet_0.1.0 nlme_3.1-137 jsonlite_1.6.1 gtable_0.2.0
[41] lifecycle_0.2.0 magrittr_1.5 scales_1.1.0 cli_2.0.2
[45] stringi_1.2.4 farver_2.0.3 doParallel_1.0.15 vctrs_0.2.4
[49] cowplot_0.9.99 Rhdf5lib_1.2.1 RColorBrewer_1.1-2 iterators_1.0.10
[53] tools_3.5.1 glue_1.3.0 purrr_0.3.3 network_1.16.0
[57] parallel_3.5.1 yaml_2.2.0 colorspace_1.3-2 rhdf5_2.24.0
[61] cluster_2.0.7-1 plotly_4.9.2

I searched google to try to fix it but failed. Does anyone has ever got the same problem? Any suggestions would be greatly appreciated. Thanks in advance!

[KasperSkytte]

Hi there

The .onAttach() function will print the current ampvis2 version when you load it and check for new version. I have used remotes for quite some time to do that, but due to issues like this, when no internet connection, or as in your case namespace issues with the remotes package, I changed the implementation to avoid using remotes. So if you just update ampvis2 to 2.5.5 or later it should work just fine, let me know if not.

[Jessie-HOU]

Dear Andersen,

I checked and found the version of ampvis2 I installed is 2.6.0. The same problem exists even for this version.

Best regards, Jessie

On Thu, May 7, 2020 at 3:51 PM Kasper Skytte Andersen < notifications@github.com> wrote:

Hi there

The .onAttach() function will print the current ampvis2 version when you load it and check for new version. I have used remotes for quite some time to do that, but due to issues like this, when no internet connection, or as in your case namespace issues with the remotes package, I changed the implementation to avoid using remotes. So if you just update ampvis2 to 2.5.5 or later it should work just fine, let me know if not.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MadsAlbertsen/ampvis2/issues/92#issuecomment-625092057, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHE7VREN7OBMHU3KXFNEGIDRQJSBNANCNFSM4M2HY7PA .

[KasperSkytte]

Sorry I totally forgot about this. But I see the issue now, will post a fix soon. It will only occur when you have no internet connection though.

[KasperSkytte]

Fixed in 2f4d8338ca8b927d08f9871cc26b8c6269039cd3

[Jessie-HOU]

Dear Andersen,

Thank you for your reply. I install ampvis2 v2.6.1 in Rstudio. However, I cannot find the help page for this package. Then I tried to re-install it, but got the following error messages:

options(download.file.method = "auto") remotes::install_github("MadsAlbertsen/ampvis2",force = TRUE) Downloading GitHub repo MadsAlbertsen/ampvis2@master Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL ' https://api.github.com/repos/MadsAlbertsen/ampvis2/tarball/master' options(download.file.method = "internal") remotes::install_github("MadsAlbertsen/ampvis2",force = TRUE) Downloading GitHub repo MadsAlbertsen/ampvis2@master Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL ' http://api.github.com/repos/MadsAlbertsen/ampvis2/tarball/master' options(download.file.method = "wget") remotes::install_github("MadsAlbertsen/ampvis2",force = TRUE) Downloading GitHub repo MadsAlbertsen/ampvis2@master Error in utils::download.file(url, path, method = "wget", quiet = quiet, : 'wget' call had nonzero exit status

Here is some of my R environment:

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] ampvis2_2.6.1 ggplot2_3.3.0

loaded via a namespace (and not attached): [1] network_1.16.0 tidyselect_1.0.0 remotes_2.1.1 purrr_0.3.3 lattice_0.20-35

I don't know where the problem is. Sorry for bothering you always. Thank you so much!

Best regards, Jessie

On Thu, May 14, 2020 at 4:39 PM Kasper Skytte Andersen < notifications@github.com> wrote:

Closed #92 https://github.com/MadsAlbertsen/ampvis2/issues/92.

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[KasperSkytte]

Hi again. Seems like you are having network problems. You cannot seem to contact github.