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error code 60 leds renv to ask to reinstall packages #1948

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llrs opened this issue Jul 23, 2024 · 4 comments
Closed

error code 60 leds renv to ask to reinstall packages #1948

llrs opened this issue Jul 23, 2024 · 4 comments

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@llrs
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llrs commented Jul 23, 2024

I am working on a project using R 4.4.0 and renv '1.0.7.9000' and I am facing a problem related to Bioconductor.

I think it might be related to #1920 (or #1943):

  1. MASS is detected as the same version of the lock file but still asks me about it because "installed from an unknown source".
  2. When creating the snapshot many Bioconductor packages appear off and I get a warning to reinstall them while the problem is that the repository data couldn't be retrieved.

Is there a work around this? This might be due to the proxy in my workplace, but I haven't faced any problem to install packages or doing some other operations (but I had problems with some programs requiring internet connection).

 renv::status()
renv was unable to query available packages from the following repositories:
- # https://bioconductor.org/packages/3.19/bioc/src/contrib --------------------
error downloading 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES' [error code 60]

- # https://bioconductor.org/packages/3.19/books/src/contrib -------------------
error downloading 'https://bioconductor.org/packages/3.19/books/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/books/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/books/src/contrib/PACKAGES' [error code 60]

- # https://cloud.r-project.org/src/contrib ------------------------------------
error downloading 'https://cloud.r-project.org/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://cloud.r-project.org/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://cloud.r-project.org/src/contrib/PACKAGES' [error code 60]

- # https://bioconductor.org/packages/3.19/data/experiment/src/contrib ---------
error downloading 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES' [error code 60]

- # https://bioconductor.org/packages/3.19/data/annotation/src/contrib ---------
error downloading 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES' [error code 60]

- # https://packagemanager.rstudio.com/all/__linux__/jammy/latest/src/contrib --------
error downloading 'https://packagemanager.rstudio.com/all/__linux__/jammy/latest/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://packagemanager.rstudio.com/all/__linux__/jammy/latest/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://packagemanager.rstudio.com/all/__linux__/jammy/latest/src/contrib/PACKAGES' [error code 60]

- # https://bioconductor.org/packages/3.19/workflows/src/contrib ---------------
error downloading 'https://bioconductor.org/packages/3.19/workflows/src/contrib/PACKAGES.rds' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/workflows/src/contrib/PACKAGES.gz' [error code 60]
error downloading 'https://bioconductor.org/packages/3.19/workflows/src/contrib/PACKAGES' [error code 60]


The following package(s) are in an inconsistent state:

 package        installed recorded used
 batchelor      y         n        y   
 ResidualMatrix y         n        y   

The following package(s) are out of sync [lockfile != library]:

# GitHub ---------------------------------------------------------------------
- rutils   [ver: 0.0.1.9004 != 0.0.1.9007; ref: master != HEAD; sha: 6263a9ff != 46812079]

# (Unknown Source) -----------------------------------------------------------
- MASS     [7.3-60.2 != 7.3-60.2]

See ?renv::status() for advice on resolving these issues.
renv::diagnostics()
Diagnostics Report [renv 1.0.7.9000 [sha: 1f99d7d]]
===================================================

# /etc/lsb-release -----------------------------------------------------------
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.4 LTS"

# /etc/os-release ------------------------------------------------------------
PRETTY_NAME="Ubuntu 22.04.4 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.4 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy


# Session Info ---------------------------------------------------------------
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

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

other attached packages:
[1] readxl_1.4.3      dplyr_1.1.4       rutils_0.0.1.9007 targets_1.7.1    

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5         cli_3.6.3           knitr_1.47         
 [4] rlang_1.1.4         xfun_0.45           processx_3.8.4     
 [7] generics_0.1.3      renv_1.0.7.9000     data.table_1.15.4  
[10] glue_1.7.0          backports_1.5.0     ps_1.7.6           
[13] fansi_1.0.6         cellranger_1.1.0    tibble_3.2.1       
[16] base64url_1.4       yaml_2.3.8          lifecycle_1.0.4    
[19] BiocManager_1.30.23 compiler_4.4.0      codetools_0.2-20   
[22] igraph_2.0.3        pkgconfig_2.0.3     rstudioapi_0.16.0  
[25] R6_2.5.1            tidyselect_1.2.1    utf8_1.2.4         
[28] pillar_1.9.0        callr_3.7.6         magrittr_2.0.3     
[31] withr_3.0.0         tools_4.4.0         secretbase_1.0.0   

# Project --------------------------------------------------------------------
Project path: "~/Documents/projects/EpiNeuro"

# Status ---------------------------------------------------------------------
The following package(s) are in an inconsistent state:

 package        installed recorded used
 batchelor      y         n        y   
 ResidualMatrix y         n        y   

The following package(s) are out of sync [lockfile != library]:

# GitHub ---------------------------------------------------------------------
- rutils   [ver: 0.0.1.9004 != 0.0.1.9007; ref: master != HEAD; sha: 6263a9ff != 46812079]

# (Unknown Source) -----------------------------------------------------------
- MASS     [7.3-60.2 != 7.3-60.2]

See ?renv::status() for advice on resolving these issues.

# Packages -------------------------------------------------------------------
                        Library            Source   Lockfile            Source Path Dependency
AUCell                   1.26.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
AnnotationDbi            1.66.0 Bioconductor 3.19     1.66.0 Bioconductor 3.19  [1]   indirect
AnnotationFilter         1.28.0 Bioconductor 3.19     1.28.0 Bioconductor 3.19  [1]   indirect
AnnotationHub            3.12.0 Bioconductor 3.19     3.12.0 Bioconductor 3.19  [1]     direct
BH                     1.84.0-0              RSPM   1.84.0-0              RSPM  [1]   indirect
Biobase                  2.64.0 Bioconductor 3.19     2.64.0 Bioconductor 3.19  [1]   indirect
BiocFileCache            2.12.0 Bioconductor 3.19     2.12.0 Bioconductor 3.19  [1]   indirect
BiocGenerics             0.50.0 Bioconductor 3.19     0.50.0 Bioconductor 3.19  [1]   indirect
BiocIO                   1.14.0 Bioconductor 3.19     1.14.0 Bioconductor 3.19  [1]   indirect
BiocManager             1.30.23              RSPM    1.30.23              RSPM  [1]   indirect
BiocNeighbors            1.22.0 Bioconductor 3.19     1.22.0 Bioconductor 3.19  [1]   indirect
BiocParallel             1.38.0 Bioconductor 3.19     1.38.0 Bioconductor 3.19  [1]     direct
BiocSingular             1.20.0 Bioconductor 3.19     1.20.0 Bioconductor 3.19  [1]     direct
BiocVersion              3.19.1 Bioconductor 3.19     3.19.1 Bioconductor 3.19  [1]   indirect
Biostrings               2.72.1 Bioconductor 3.19     2.72.1 Bioconductor 3.19  [1]   indirect
Cairo                     1.6-2              RSPM      1.6-2              RSPM  [1]   indirect
ClusterR                  1.3.3              RSPM       <NA>              <NA>  [1]       <NA>
DBI                       1.2.3              RSPM      1.2.3              RSPM  [1]   indirect
DEoptimR                  1.1-3              RSPM      1.1-3              RSPM  [1]   indirect
DT                         0.33              RSPM       <NA>              <NA>  [1]       <NA>
DelayedArray             0.30.1 Bioconductor 3.19     0.30.1 Bioconductor 3.19  [1]   indirect
DelayedMatrixStats       1.26.0 Bioconductor 3.19     1.26.0 Bioconductor 3.19  [1]     direct
DropletUtils             1.24.0 Bioconductor 3.19     1.24.0 Bioconductor 3.19  [1]     direct
ExperimentHub            2.12.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
FNN                       1.1.4              RSPM      1.1.4              RSPM  [1]   indirect
Formula                   1.2-5              RSPM       <NA>              <NA>  [1]       <NA>
GO.db                    3.19.1      Bioconductor     3.19.1      Bioconductor  [1]     direct
GSEABase                 1.66.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
GenomeInfoDb             1.40.1 Bioconductor 3.19     1.40.1 Bioconductor 3.19  [1]   indirect
GenomeInfoDbData         1.2.12      Bioconductor     1.2.12      Bioconductor  [1]   indirect
GenomicAlignments        1.40.0 Bioconductor 3.19     1.40.0 Bioconductor 3.19  [1]   indirect
GenomicFeatures          1.56.0 Bioconductor 3.19     1.56.0 Bioconductor 3.19  [1]   indirect
GenomicRanges            1.56.1 Bioconductor 3.19     1.56.1 Bioconductor 3.19  [1]   indirect
HDF5Array                1.32.0 Bioconductor 3.19     1.32.0 Bioconductor 3.19  [1]     direct
Hmisc                     5.1-3              RSPM       <NA>              <NA>  [1]       <NA>
IRanges                  2.38.0 Bioconductor 3.19     2.38.0 Bioconductor 3.19  [1]   indirect
KEGGREST                 1.44.1 Bioconductor 3.19     1.44.1 Bioconductor 3.19  [1]   indirect
KernSmooth              2.23-22              CRAN       <NA>              <NA>  [2]       <NA>
MASS                   7.3-60.2           unknown   7.3-60.2              RSPM  [2]     direct
Matrix                    1.7-0              CRAN      1.7-0              CRAN  [2]   indirect
MatrixGenerics           1.16.0 Bioconductor 3.19     1.16.0 Bioconductor 3.19  [1]   indirect
MatrixModels              0.5-3              RSPM      0.5-3              RSPM  [1]   indirect
NMF                        0.27              RSPM       <NA>              <NA>  [1]       <NA>
PCAtools                 2.16.0 Bioconductor 3.19     2.16.0 Bioconductor 3.19  [1]     direct
ProtGenerics             1.36.0 Bioconductor 3.19     1.36.0 Bioconductor 3.19  [1]   indirect
R.methodsS3               1.8.2              RSPM      1.8.2              RSPM  [1]   indirect
R.oo                     1.26.0              RSPM     1.26.0              RSPM  [1]   indirect
R.utils                  2.12.3              RSPM     2.12.3              RSPM  [1]   indirect
R2HTML                    2.3.4              RSPM       <NA>              <NA>  [1]       <NA>
R6                        2.5.1              RSPM      2.5.1              RSPM  [1]   indirect
RANN                      2.6.1              RSPM       <NA>              <NA>  [1]       <NA>
RColorBrewer              1.1-3              RSPM      1.1-3              RSPM  [1]   indirect
RCurl                 1.98-1.14              RSPM  1.98-1.14              RSPM  [1]   indirect
RMariaDB                  1.3.2              RSPM       <NA>              <NA>  [1]       <NA>
ROCR                     1.0-11              RSPM       <NA>              <NA>  [1]       <NA>
RSQLite                   2.3.7              RSPM      2.3.7              RSPM  [1]   indirect
RSpectra                 0.16-1              RSPM     0.16-1              RSPM  [1]   indirect
Rcpp                     1.0.12              RSPM     1.0.12              RSPM  [1]   indirect
RcppAnnoy                0.0.22              RSPM     0.0.22              RSPM  [1]   indirect
RcppArmadillo        0.12.8.4.0              RSPM 0.12.8.4.0              RSPM  [1]   indirect
RcppEigen             0.3.4.0.0              RSPM  0.3.4.0.0              RSPM  [1]   indirect
RcppHNSW                  0.6.0              RSPM      0.6.0              RSPM  [1]   indirect
RcppML                    0.3.7              RSPM      0.3.7              RSPM  [1]   indirect
RcppProgress              0.4.2              RSPM      0.4.2              RSPM  [1]   indirect
RcppTOML                  0.2.2              RSPM       <NA>              <NA>  [1]       <NA>
ResidualMatrix           1.14.1 Bioconductor 3.19       <NA>              <NA>  [1]   indirect
Rhdf5lib                 1.26.0 Bioconductor 3.19     1.26.0 Bioconductor 3.19  [1]   indirect
RhpcBLASctl             0.23-42              RSPM       <NA>              <NA>  [1]       <NA>
Rhtslib                   3.0.0 Bioconductor 3.19      3.0.0 Bioconductor 3.19  [1]   indirect
Rsamtools                2.20.0 Bioconductor 3.19     2.20.0 Bioconductor 3.19  [1]   indirect
Rtsne                      0.17              RSPM       0.17              RSPM  [1]   indirect
S4Arrays                  1.4.1 Bioconductor 3.19      1.4.1 Bioconductor 3.19  [1]   indirect
S4Vectors                0.42.0 Bioconductor 3.19     0.42.0 Bioconductor 3.19  [1]   indirect
ScaledMatrix             1.12.0 Bioconductor 3.19     1.12.0 Bioconductor 3.19  [1]   indirect
Seurat                    5.1.0              RSPM       <NA>              <NA>  [1]       <NA>
SeuratObject              5.0.2              CRAN      5.0.2              CRAN  [1]   indirect
SingleCellExperiment     1.26.0 Bioconductor 3.19     1.26.0 Bioconductor 3.19  [1]   indirect
SingleR                   2.6.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
SoupX                     1.6.2              RSPM       <NA>              <NA>  [1]       <NA>
SparseArray               1.4.8 Bioconductor 3.19      1.4.8 Bioconductor 3.19  [1]   indirect
SparseM                    1.84              RSPM       1.84              RSPM  [1]   indirect
SummarizedExperiment     1.34.0 Bioconductor 3.19     1.34.0 Bioconductor 3.19  [1]   indirect
UCSC.utils                1.0.0 Bioconductor 3.19      1.0.0 Bioconductor 3.19  [1]   indirect
V8                        4.4.2              RSPM       <NA>              <NA>  [1]       <NA>
VGAM                     1.1-11              RSPM     1.1-11              RSPM  [1]   indirect
XML                   3.99-0.17              RSPM  3.99-0.17              RSPM  [1]   indirect
XVector                  0.44.0 Bioconductor 3.19     0.44.0 Bioconductor 3.19  [1]   indirect
abind                     1.4-5              RSPM      1.4-5              RSPM  [1]   indirect
alabaster.base            1.4.2 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
alabaster.matrix          1.4.2 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
alabaster.ranges          1.4.2 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
alabaster.sce             1.4.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
alabaster.schemas         1.4.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
alabaster.se              1.4.1 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
annotate                 1.82.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
apcluster                1.4.13              RSPM       <NA>              <NA>  [1]       <NA>
askpass                   1.2.0              RSPM      1.2.0              RSPM  [1]   indirect
backports                 1.5.0              RSPM      1.5.0              RSPM  [1]   indirect
base64enc                 0.1-3              RSPM      0.1-3              RSPM  [1]   indirect
base64url                   1.4              RSPM        1.4              CRAN  [1]   indirect
batchelor                1.20.0 Bioconductor 3.19       <NA>              <NA>  [1]     direct
beachmat                 2.20.0 Bioconductor 3.19     2.20.0 Bioconductor 3.19  [1]   indirect
beeswarm                  0.4.0              RSPM      0.4.0              RSPM  [1]   indirect
benchmarkme               1.0.8              RSPM       <NA>              <NA>  [1]       <NA>
benchmarkmeData           1.0.4              RSPM       <NA>              <NA>  [1]       <NA>
biomaRt                  2.60.0 Bioconductor 3.19     2.60.0 Bioconductor 3.19  [1]     direct
bit                       4.0.5              RSPM      4.0.5              RSPM  [1]   indirect
bit64                     4.0.5              RSPM      4.0.5              RSPM  [1]   indirect
bitops                    1.0-7              RSPM      1.0-7              RSPM  [1]   indirect
blob                      1.2.4              RSPM      1.2.4              RSPM  [1]   indirect
bluster                  1.14.0 Bioconductor 3.19     1.14.0 Bioconductor 3.19  [1]     direct
boot                     1.3-30              CRAN       <NA>              <NA>  [2]       <NA>
brio                      1.1.5              RSPM       <NA>              <NA>  [1]       <NA>
broom                     1.0.6              RSPM      1.0.6              RSPM  [1]     direct
bslib                     0.7.0              RSPM      0.7.0              RSPM  [1]   indirect
caTools                  1.18.2              RSPM       <NA>              <NA>  [1]       <NA>
cachem                    1.1.0              RSPM      1.1.0              RSPM  [1]   indirect
callr                     3.7.6              RSPM      3.7.6              RSPM  [1]   indirect
celldex                  1.14.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
cellranger                1.1.0              RSPM      1.1.0              RSPM  [1]   indirect
checkmate                 2.3.1              RSPM      2.3.1              RSPM  [1]   indirect
class                    7.3-22              CRAN       <NA>              <NA>  [2]       <NA>
cli                       3.6.3              RSPM      3.6.3              RSPM  [1]   indirect
clipr                     0.8.0              RSPM      0.8.0              RSPM  [1]   indirect
cluster                   2.1.6              CRAN      2.1.6              CRAN  [2]   indirect
clustree                  0.5.1              RSPM      0.5.1              RSPM  [1]     direct
codetools                0.2-20              CRAN     0.2-20              CRAN  [2]   indirect
colorspace                2.1-0              RSPM      2.1-0              RSPM  [1]   indirect
commonmark                1.9.1              RSPM       <NA>              <NA>  [1]       <NA>
compiler                   <NA>              <NA>       <NA>              <NA>  [2]   indirect
conflicted                1.2.0              RSPM      1.2.0              RSPM  [1]   indirect
cowplot                   1.1.3              RSPM      1.1.3              RSPM  [1]   indirect
cpp11                     0.4.7              RSPM      0.4.7              RSPM  [1]   indirect
crayon                    1.5.3              RSPM      1.5.3              RSPM  [1]   indirect
credentials               2.0.1              RSPM      2.0.1              RSPM  [1]   indirect
crosstalk                 1.2.1              RSPM       <NA>              <NA>  [1]       <NA>
cubature                  2.1.0              RSPM      2.1.0              RSPM  [1]   indirect
curl                      5.2.1              RSPM      5.2.1              RSPM  [1]   indirect
data.table               1.15.4              RSPM     1.15.4              RSPM  [1]     direct
dbplyr                    2.5.0              RSPM      2.5.0              RSPM  [1]   indirect
deldir                    2.0-4              RSPM       <NA>              <NA>  [1]       <NA>
desc                      1.4.3              CRAN       <NA>              <NA>  [1]       <NA>
diffobj                   0.3.5              RSPM       <NA>              <NA>  [1]       <NA>
digest                   0.6.36              RSPM     0.6.36              RSPM  [1]   indirect
doMC                      1.3.8              RSPM       <NA>              <NA>  [1]       <NA>
doParallel               1.0.17              RSPM       <NA>              <NA>  [1]       <NA>
doRNG                     1.8.6              RSPM       <NA>              <NA>  [1]       <NA>
doSNOW                   1.0.20              RSPM       <NA>              <NA>  [1]       <NA>
dotCall64                 1.1-1              RSPM      1.1-1              RSPM  [1]   indirect
downlit                   0.4.4              RSPM       <NA>              <NA>  [1]       <NA>
dplyr                     1.1.4              RSPM      1.1.4              RSPM  [1]     direct
dqrng                     0.4.1              RSPM      0.4.1              RSPM  [1]   indirect
dtplyr                    1.3.1              RSPM      1.3.1              RSPM  [1]   indirect
dynamicTreeCut           1.63-1              RSPM       <NA>              <NA>  [1]       <NA>
edgeR                     4.2.0 Bioconductor 3.19      4.2.0 Bioconductor 3.19  [1]   indirect
ensembldb                2.28.0 Bioconductor 3.19     2.28.0 Bioconductor 3.19  [1]     direct
evaluate                 0.24.0              RSPM     0.24.0              RSPM  [1]   indirect
evd                       2.3-7              RSPM      2.3-7              RSPM  [1]   indirect
evmix                      2.12              RSPM       2.12              RSPM  [1]   indirect
fansi                     1.0.6              RSPM      1.0.6              RSPM  [1]   indirect
farver                    2.1.2              RSPM      2.1.2              RSPM  [1]   indirect
fastDummies               1.7.3              RSPM       <NA>              <NA>  [1]       <NA>
fastmap                   1.2.0              RSPM      1.2.0              RSPM  [1]   indirect
filelock                  1.0.3              RSPM      1.0.3              RSPM  [1]   indirect
fitdistrplus             1.1-11              RSPM       <NA>              <NA>  [1]       <NA>
fontawesome               0.5.2              RSPM      0.5.2              RSPM  [1]   indirect
forcats                   1.0.0              RSPM      1.0.0              RSPM  [1]     direct
foreach                   1.5.2              RSPM       <NA>              <NA>  [1]       <NA>
foreign                  0.8-86              CRAN       <NA>              <NA>  [2]       <NA>
formatR                    1.14              RSPM       1.14              RSPM  [1]   indirect
fs                        1.6.4              RSPM      1.6.4              RSPM  [1]   indirect
futile.logger             1.4.3              RSPM      1.4.3              RSPM  [1]   indirect
futile.options            1.0.1              RSPM      1.0.1              RSPM  [1]   indirect
future                   1.33.2              RSPM     1.33.2              RSPM  [1]   indirect
future.apply             1.11.2              RSPM     1.11.2              RSPM  [1]   indirect
gargle                    1.5.2              RSPM      1.5.2              RSPM  [1]   indirect
generics                  0.1.3              RSPM      0.1.3              RSPM  [1]   indirect
gert                      2.0.1              RSPM      2.0.1              RSPM  [1]   indirect
ggalluvial               0.12.5              RSPM     0.12.5              RSPM  [1]   indirect
ggbeeswarm                0.7.2              RSPM      0.7.2              RSPM  [1]   indirect
ggblend                   0.1.0              RSPM      0.1.0              RSPM  [1]     direct
ggdendro                  0.2.0              RSPM      0.2.0              RSPM  [1]   indirect
ggforce                   0.4.2              RSPM      0.4.2              RSPM  [1]     direct
ggplot2                   3.5.1              RSPM      3.5.1              RSPM  [1]     direct
ggraph                    2.2.1              RSPM      2.2.1              RSPM  [1]   indirect
ggrastr                   1.0.2              RSPM      1.0.2              RSPM  [1]   indirect
ggrepel                   0.9.5              RSPM      0.9.5              RSPM  [1]   indirect
ggridges                  0.5.6              RSPM       <NA>              <NA>  [1]       <NA>
gittargets                0.0.7              RSPM      0.0.7              RSPM  [1]     direct
globals                  0.16.3              RSPM     0.16.3              RSPM  [1]   indirect
glue                      1.7.0              RSPM      1.7.0              RSPM  [1]   indirect
gmp                       0.7-4              RSPM       <NA>              <NA>  [1]       <NA>
goftest                   1.2-3              RSPM       <NA>              <NA>  [1]       <NA>
googledrive               2.1.1              RSPM      2.1.1              RSPM  [1]   indirect
googlesheets4             1.1.1              RSPM      1.1.1              RSPM  [1]   indirect
gplots                  3.1.3.1              RSPM       <NA>              <NA>  [1]       <NA>
grDevices                  <NA>              <NA>       <NA>              <NA>  [2]   indirect
graph                    1.82.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
graphics                   <NA>              <NA>       <NA>              <NA>  [2]   indirect
graphlayouts              1.1.1              RSPM      1.1.1              RSPM  [1]   indirect
grid                       <NA>              <NA>       <NA>              <NA>  [2]   indirect
gridBase                  0.4-7              RSPM       <NA>              <NA>  [1]       <NA>
gridExtra                   2.3              RSPM        2.3              RSPM  [1]   indirect
gsl                       2.1-8              RSPM      2.1-8              RSPM  [1]   indirect
gtable                    0.3.5              RSPM      0.3.5              RSPM  [1]   indirect
gtools                    3.9.5              RSPM       <NA>              <NA>  [1]       <NA>
gypsum                    1.0.1 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
harmony                   1.2.0              RSPM       <NA>              <NA>  [1]       <NA>
hash                    2.2.6.3              RSPM    2.2.6.3              RSPM  [1]   indirect
haven                     2.5.4              RSPM      2.5.4              RSPM  [1]   indirect
here                      1.0.1              RSPM      1.0.1              RSPM  [1]     direct
hexbin                   1.28.3              RSPM     1.28.3              RSPM  [1]     direct
highr                      0.11              RSPM       0.11              RSPM  [1]   indirect
hms                       1.1.3              RSPM      1.1.3              RSPM  [1]   indirect
htmlTable                 2.4.2              RSPM       <NA>              <NA>  [1]       <NA>
htmltools               0.5.8.1              RSPM    0.5.8.1              RSPM  [1]   indirect
htmlwidgets               1.6.4              RSPM       <NA>              <NA>  [1]       <NA>
httpuv                   1.6.15              RSPM       <NA>              <NA>  [1]       <NA>
httr                      1.4.7              RSPM      1.4.7              RSPM  [1]   indirect
httr2                     1.0.1              RSPM      1.0.1              RSPM  [1]   indirect
iNEXT                     3.0.1              RSPM      3.0.1              RSPM  [1]   indirect
ica                       1.0-3              RSPM       <NA>              <NA>  [1]       <NA>
ids                       1.0.1              RSPM      1.0.1              RSPM  [1]   indirect
igraph                    2.0.3              RSPM      2.0.3              RSPM  [1]   indirect
irlba                   2.3.5.1              RSPM    2.3.5.1              RSPM  [1]   indirect
isoband                   0.2.7              RSPM      0.2.7              RSPM  [1]   indirect
iterators                1.0.14              RSPM       <NA>              <NA>  [1]       <NA>
jquerylib                 0.1.4              RSPM      0.1.4              RSPM  [1]   indirect
jsonlite                  1.8.8              RSPM      1.8.8              RSPM  [1]   indirect
jsonvalidate              1.3.2              RSPM       <NA>              <NA>  [1]       <NA>
kernlab                  0.9-32              RSPM       <NA>              <NA>  [1]       <NA>
knitr                      1.47              RSPM       1.47              RSPM  [1]     direct
labeling                  0.4.3              RSPM      0.4.3              RSPM  [1]   indirect
lambda.r                  1.2.4              RSPM      1.2.4              RSPM  [1]   indirect
later                     1.3.2              RSPM       <NA>              <NA>  [1]       <NA>
lattice                  0.22-6              CRAN     0.22-6              CRAN  [2]   indirect
lazyeval                  0.2.2              RSPM      0.2.2              RSPM  [1]   indirect
leiden                  0.4.3.1              RSPM       <NA>              <NA>  [1]       <NA>
lifecycle                 1.0.4              RSPM      1.0.4              RSPM  [1]   indirect
limma                    3.60.3 Bioconductor 3.19     3.60.3 Bioconductor 3.19  [1]   indirect
listenv                   0.9.1              RSPM      0.9.1              RSPM  [1]   indirect
lmtest                   0.9-40              RSPM       <NA>              <NA>  [1]       <NA>
locfit                 1.5-9.10              RSPM   1.5-9.10              RSPM  [1]   indirect
lubridate                 1.9.3              RSPM      1.9.3              RSPM  [1]   indirect
magrittr                  2.0.3              RSPM      2.0.3              RSPM  [1]   indirect
matrixStats               1.3.0              RSPM      1.3.0              RSPM  [1]   indirect
mbkmeans                 1.20.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
memoise                   2.0.1              RSPM      2.0.1              RSPM  [1]   indirect
metapod                  1.12.0 Bioconductor 3.19     1.12.0 Bioconductor 3.19  [1]   indirect
methods                    <NA>              <NA>       <NA>              <NA>  [2]   indirect
mgcv                      1.9-1              CRAN      1.9-1              CRAN  [2]   indirect
mime                       0.12              RSPM       0.12              RSPM  [1]   indirect
miniUI                  0.1.1.1              RSPM       <NA>              <NA>  [1]       <NA>
mixtools                  2.0.0              RSPM       <NA>              <NA>  [1]       <NA>
modelr                   0.1.11              RSPM     0.1.11              RSPM  [1]   indirect
munsell                   0.5.1              RSPM      0.5.1              RSPM  [1]   indirect
nlme                    3.1-164              CRAN    3.1-164              CRAN  [2]   indirect
nnet                     7.3-19              CRAN       <NA>              <NA>  [2]       <NA>
openssl                   2.2.0              RSPM      2.2.0              RSPM  [1]   indirect
pROC                     1.18.5              RSPM     1.18.5              RSPM  [1]   indirect
parallel                   <NA>              <NA>       <NA>              <NA>  [2]   indirect
parallelly               1.37.1              RSPM     1.37.1              RSPM  [1]   indirect
patchwork                 1.2.0              RSPM      1.2.0              RSPM  [1]     direct
pbapply                   1.7-2              RSPM       <NA>              <NA>  [1]       <NA>
pheatmap                 1.0.12              RSPM     1.0.12              RSPM  [1]   indirect
pillar                    1.9.0              RSPM      1.9.0              RSPM  [1]   indirect
pkgconfig                 2.0.3              RSPM      2.0.3              RSPM  [1]   indirect
plogr                     0.2.0              RSPM      0.2.0              RSPM  [1]   indirect
plotly                   4.10.4              RSPM       <NA>              <NA>  [1]       <NA>
plyr                      1.8.9              RSPM      1.8.9              RSPM  [1]   indirect
png                       0.1-8              RSPM      0.1-8              RSPM  [1]   indirect
polyclip                 1.10-6              RSPM     1.10-6              RSPM  [1]   indirect
prettyunits               1.2.0              RSPM      1.2.0              RSPM  [1]   indirect
processx                  3.8.4              RSPM      3.8.4              RSPM  [1]   indirect
progress                  1.2.3              RSPM      1.2.3              RSPM  [1]   indirect
progressr                0.14.0              RSPM     0.14.0              RSPM  [1]   indirect
promises                  1.3.0              RSPM       <NA>              <NA>  [1]       <NA>
ps                        1.7.6              RSPM      1.7.6              RSPM  [1]   indirect
purrr                     1.0.2              RSPM      1.0.2              RSPM  [1]   indirect
quantreg                   5.98              RSPM       5.98              RSPM  [1]   indirect
quarto                      1.4              CRAN       <NA>              <NA>  [1]       <NA>
ragg                      1.3.2              RSPM      1.3.2              RSPM  [1]     direct
rappdirs                  0.3.3              RSPM      0.3.3              RSPM  [1]   indirect
readr                     2.1.5              RSPM      2.1.5              RSPM  [1]   indirect
readxl                    1.4.3              RSPM      1.4.3              RSPM  [1]     direct
registry                  0.5-1              RSPM       <NA>              <NA>  [1]       <NA>
rematch                   2.0.0              RSPM      2.0.0              RSPM  [1]   indirect
rematch2                  2.1.2              RSPM      2.1.2              RSPM  [1]   indirect
remotes                   2.5.0              RSPM       <NA>              <NA>  [1]       <NA>
renv                 1.0.7.9000            GitHub 1.0.7.9000            GitHub  [1]     direct
reprex                    2.1.0              RSPM      2.1.0              RSPM  [1]   indirect
reshape2                  1.4.4              RSPM      1.4.4              RSPM  [1]   indirect
restfulr                 0.0.15              RSPM     0.0.15              RSPM  [1]   indirect
reticulate               1.38.0              RSPM       <NA>              <NA>  [1]       <NA>
rhdf5                    2.48.0 Bioconductor 3.19     2.48.0 Bioconductor 3.19  [1]     direct
rhdf5filters             1.16.0 Bioconductor 3.19     1.16.0 Bioconductor 3.19  [1]   indirect
rjson                    0.2.21              RSPM     0.2.21              RSPM  [1]   indirect
rlang                     1.1.4              RSPM      1.1.4              RSPM  [1]   indirect
rmarkdown                  2.27              RSPM       2.27              RSPM  [1]     direct
rngtools                  1.5.2              RSPM       <NA>              <NA>  [1]       <NA>
robustbase               0.99-2              RSPM     0.99-2              RSPM  [1]     direct
rpart                    4.1.23              CRAN       <NA>              <NA>  [2]       <NA>
rprojroot                 2.0.4              RSPM      2.0.4              RSPM  [1]   indirect
rstudioapi               0.16.0              RSPM     0.16.0              RSPM  [1]   indirect
rsvd                      1.0.5              RSPM      1.0.5              RSPM  [1]   indirect
rtracklayer              1.64.0 Bioconductor 3.19     1.64.0 Bioconductor 3.19  [1]   indirect
rutils               0.0.1.9007            GitHub 0.0.1.9004            GitHub  [1]     direct
rvest                     1.0.4              RSPM      1.0.4              RSPM  [1]   indirect
sass                      0.4.9              RSPM      0.4.9              RSPM  [1]   indirect
scDblFinder              1.18.0 Bioconductor 3.19     1.18.0 Bioconductor 3.19  [1]     direct
scRNAseq                 2.18.0 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
scRepertoire              2.0.0            GitHub      2.0.0            GitHub  [1]     direct
scales                    1.3.0              RSPM      1.3.0              RSPM  [1]     direct
scater                   1.32.0 Bioconductor 3.19     1.32.0 Bioconductor 3.19  [1]     direct
scattermore                 1.2              RSPM       <NA>              <NA>  [1]       <NA>
scds                     1.20.0 Bioconductor 3.19     1.20.0 Bioconductor 3.19  [1]     direct
scran                    1.32.0 Bioconductor 3.19     1.32.0 Bioconductor 3.19  [1]     direct
sctransform               0.4.1              RSPM       <NA>              <NA>  [1]       <NA>
scuttle                  1.14.0 Bioconductor 3.19     1.14.0 Bioconductor 3.19  [1]     direct
secretbase                1.0.0              RSPM      1.0.0              RSPM  [1]   indirect
segmented                 2.1-0              RSPM       <NA>              <NA>  [1]       <NA>
selectr                   0.4-2              RSPM      0.4-2              RSPM  [1]   indirect
shiny                   1.8.1.1              RSPM       <NA>              <NA>  [1]       <NA>
sitmo                     2.0.2              RSPM      2.0.2              RSPM  [1]   indirect
snow                      0.4-4              RSPM      0.4-4              RSPM  [1]   indirect
sourcetools             0.1.7-1              RSPM       <NA>              <NA>  [1]       <NA>
sp                        2.1-4              RSPM      2.1-4              RSPM  [1]   indirect
spam                     2.10-0              RSPM     2.10-0              RSPM  [1]   indirect
sparseMatrixStats        1.16.0 Bioconductor 3.19     1.16.0 Bioconductor 3.19  [1]   indirect
spatial                  7.3-17              CRAN       <NA>              <NA>  [2]       <NA>
spatstat.data             3.1-2              RSPM       <NA>              <NA>  [1]       <NA>
spatstat.explore          3.2-7              RSPM       <NA>              <NA>  [1]       <NA>
spatstat.geom             3.2-9              RSPM       <NA>              <NA>  [1]       <NA>
spatstat.random           3.2-3              RSPM       <NA>              <NA>  [1]       <NA>
spatstat.sparse           3.1-0              RSPM       <NA>              <NA>  [1]       <NA>
spatstat.utils            3.0-5              RSPM       <NA>              <NA>  [1]       <NA>
splines                    <NA>              <NA>       <NA>              <NA>  [2]   indirect
statmod                   1.5.0              RSPM      1.5.0              RSPM  [1]   indirect
stats                      <NA>              <NA>       <NA>              <NA>  [2]   indirect
stats4                     <NA>              <NA>       <NA>              <NA>  [2]   indirect
stringdist               0.9.12              RSPM     0.9.12              RSPM  [1]   indirect
stringi                   1.8.4              RSPM      1.8.4              RSPM  [1]   indirect
stringr                   1.5.1              RSPM      1.5.1              RSPM  [1]   indirect
survival                  3.5-8              CRAN      3.5-8              CRAN  [2]   indirect
sys                       3.4.2              RSPM      3.4.2              RSPM  [1]   indirect
systemfonts               1.1.0              RSPM      1.1.0              RSPM  [1]   indirect
targets                   1.7.1              RSPM      1.7.1              RSPM  [1]     direct
tensor                      1.5              RSPM       <NA>              <NA>  [1]       <NA>
textshaping               0.4.0              RSPM      0.4.0              RSPM  [1]   indirect
tibble                    3.2.1              RSPM      3.2.1              RSPM  [1]     direct
tidygraph                 1.3.1              RSPM      1.3.1              RSPM  [1]   indirect
tidyr                     1.3.1              RSPM      1.3.1              RSPM  [1]     direct
tidyselect                1.2.1              RSPM      1.2.1              RSPM  [1]   indirect
tidyverse                 2.0.0              RSPM      2.0.0              RSPM  [1]     direct
timechange                0.3.0              RSPM      0.3.0              RSPM  [1]   indirect
tinytex                    0.51              RSPM       0.51              RSPM  [1]   indirect
tools                      <NA>              <NA>       <NA>              <NA>  [2]     direct
truncdist                 1.0-2              RSPM      1.0-2              RSPM  [1]   indirect
tweenr                    2.0.3              RSPM      2.0.3              RSPM  [1]   indirect
txdbmaker                 1.0.1 Bioconductor 3.19       <NA>              <NA>  [1]       <NA>
tzdb                      0.4.0              RSPM      0.4.0              RSPM  [1]   indirect
utf8                      1.2.4              RSPM      1.2.4              RSPM  [1]   indirect
utils                      <NA>              <NA>       <NA>              <NA>  [2]   indirect
uuid                      1.2-0              RSPM      1.2-0              RSPM  [1]   indirect
uwot                      0.2.2              RSPM      0.2.2              RSPM  [1]   indirect
vctrs                     0.6.5              RSPM      0.6.5              RSPM  [1]   indirect
vipor                     0.4.7              RSPM      0.4.7              RSPM  [1]   indirect
viridis                   0.6.5              RSPM      0.6.5              RSPM  [1]     direct
viridisLite               0.4.2              RSPM      0.4.2              RSPM  [1]   indirect
vroom                     1.6.5              RSPM      1.6.5              RSPM  [1]   indirect
waldo                     0.5.2              RSPM       <NA>              <NA>  [1]       <NA>
withr                     3.0.0              RSPM      3.0.0              RSPM  [1]   indirect
writexl                   1.5.0              RSPM      1.5.0              RSPM  [1]     direct
xfun                       0.45              RSPM       0.45              RSPM  [1]   indirect
xgboost                 1.7.7.1              RSPM    1.7.7.1              RSPM  [1]   indirect
xml2                      1.3.6              RSPM      1.3.6              RSPM  [1]   indirect
xtable                    1.8-4              RSPM       <NA>              <NA>  [1]       <NA>
yaml                      2.3.8              RSPM      2.3.8              RSPM  [1]   indirect
zip                       2.3.1              RSPM      2.3.1              RSPM  [1]   indirect
zlibbioc                 1.50.0 Bioconductor 3.19     1.50.0 Bioconductor 3.19  [1]   indirect
zoo                      1.8-12              RSPM       <NA>              <NA>  [1]       <NA>

[1]: /home/lrevilla@irsicaixa.es/Documents/projects/EpiNeuro/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
[2]: /home/lrevilla@irsicaixa.es/.cache/R/renv/sandbox/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu/3df92652          

# ABI ------------------------------------------------------------------------
The following packages were built against a newer version of Rcpp than is currently available:
- alabaster.base 1.4.2
- alabaster.matrix 1.4.2
- batchelor 1.20.0
- beachmat 2.20.0
- BiocNeighbors 1.22.0
- BiocSingular 1.20.0
- bluster 1.14.0
- DropletUtils 1.24.0
- edgeR 4.2.0
- mbkmeans 1.20.0
- metapod 1.12.0
- PCAtools 2.16.0
- scran 1.32.0
- scRepertoire 2.0.0
- scuttle 1.14.0
- SeuratObject 5.0.2
- SingleR 2.6.0
- sparseMatrixStats 1.16.0
These packages depend on Rcpp (>= 1.0.7); however, Rcpp 1.0.12 is currently installed.
Consider installing a new version of Rcpp with 'install.packages("Rcpp")'.


# User Profile ---------------------------------------------------------------
                                 Source  Package Require Version  Dev
1 /home/lrevilla@irsicaixa.es/.Rprofile devtools                 TRUE
2 /home/lrevilla@irsicaixa.es/.Rprofile  usethis                 TRUE
3 /home/lrevilla@irsicaixa.es/.Rprofile    utils                 TRUE

# Settings -------------------------------------------------------------------
List of 13
 $ bioconductor.version     : chr(0) 
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr(0) 
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ ppm.enabled              : NULL
 $ ppm.ignored.urls         : chr(0) 
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.cellar        : logi TRUE
 $ vcs.ignore.library       : logi TRUE
 $ vcs.ignore.local         : logi TRUE
 $ vcs.manage.ignores       : logi TRUE

# Options --------------------------------------------------------------------
List of 8
 $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method                : chr "libcurl"
 $ download.file.extra                 : NULL
 $ install.packages.compile.from.source: NULL
 $ pkgType                             : chr "source"
 $ repos                               : Named chr [1:7] "https://bioconductor.org/packages/3.19/bioc" "https://bioconductor.org/packages/3.19/data/annotation" "https://bioconductor.org/packages/3.19/data/experiment" "https://bioconductor.org/packages/3.19/workflows" ...
  ..- attr(*, "names")= chr [1:7] "BioCsoft" "BioCann" "BioCexp" "BioCworkflows" ...
 $ renv.consent                        : logi TRUE
 $ renv.verbose                        : logi TRUE

# Environment Variables ------------------------------------------------------
HOME                        = /home/lrevilla@irsicaixa.es
LANG                        = en_GB.UTF-8
MAKE                        = make
R_LIBS                      = <NA>
R_LIBS_SITE                 = /opt/R/4.4.0/lib/R/site-library
R_LIBS_USER                 = /home/lrevilla@irsicaixa.es/Documents/projects/EpiNeuro/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
RENV_DEFAULT_R_ENVIRON      = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS         = <NA>
RENV_DEFAULT_R_LIBS_SITE    = /opt/R/4.4.0/lib/R/site-library
RENV_DEFAULT_R_LIBS_USER    = /home/lrevilla@irsicaixa.es/R/x86_64-pc-linux-gnu-library/4.4
RENV_DEFAULT_R_PROFILE      = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT                = /home/lrevilla@irsicaixa.es/Documents/projects/EpiNeuro

# PATH -----------------------------------------------------------------------
- /home/lrevilla@irsicaixa.es/bin/mambaforge/bin
- /home/lrevilla@irsicaixa.es/bin/mambaforge/condabin
- /home/lrevilla@irsicaixa.es/perl5/bin
- /home/lrevilla@irsicaixa.es/.local/bin
- /home/lrevilla@irsicaixa.es/bin
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /sbin
- /bin
- /usr/games
- /usr/local/games
- /snap/bin
- /snap/bin
- /opt/mssql-tools18/bin
- /usr/local/go/bin
- /usr/local/go/bin/go
- /home/lrevilla@irsicaixa.es/bin
- /home/lrevilla@irsicaixa.es/bin/cellranger-7.1.0
- /opt/quarto/bin
- /usr/lib/rstudio/resources/app/bin/postback

# Cache ----------------------------------------------------------------------
There are a total of 471 packages installed in the renv cache.
Cache path: "~/.cache/R/renv/cache/v5/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu"
@kevinushey
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Collaborator

For reference, the error codes as in [error code 60] are coming from curl, and usually implies some sort of certificate issue. (Unfortunately, we're losing out on the exact issue here...)

Do you see an error if you invoke curl by hand, e.g. with

system("curl https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES > /dev/null")

I'm less certain about MASS here... what is the output of:

packageDescription("MASS")

Normally, it should have a field like Repository: CRAN -- presumedly that's missing in this case?

@llrs
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Author

llrs commented Jul 23, 2024

I understand that the error is on curl/connectivity side, my issue is that it prompts to install packages from source if I do renv::snapshot() (Sorry I think I edited that part out of the initial code block).

From Rstudio:

 system("curl https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES > /dev/null")
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (60) SSL certificate problem: self signed certificate in certificate chain
More details here: https://curl.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.

But from the bash terminal or raw R terminal I don't have that certificate issue problem:

$ curl https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES > /dev/null
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  828k  100  828k    0     0  1071k      0 --:--:-- --:--:-- --:--:-- 1071k

Here is the DESCRIPTION file (it doesn't have the Repository:CRAN field):

Package: MASS
Priority: recommended
Version: 7.3-60.2
Date: 2024-01-12
Revision: $Rev: 3641 $
Depends: R (>= 4.4.0), grDevices, graphics, stats, utils
Imports: methods
Suggests: lattice, nlme, nnet, survival
Authors@R: c(person("Brian", "Ripley", role = c("aut", "cre",
       "cph"), email = "ripley@stats.ox.ac.uk"), person("Bill",
       "Venables", role = "ctb"), person(c("Douglas", "M."),
       "Bates", role = "ctb"), person("Kurt", "Hornik", role =
       "trl", comment = "partial port ca 1998"),
       person("Albrecht", "Gebhardt", role = "trl", comment =
       "partial port ca 1998"), person("David", "Firth", role =
       "ctb"))
Description: Functions and datasets to support Venables and
       Ripley, "Modern Applied Statistics with S" (4th edition,
       2002).
Title: Support Functions and Datasets for Venables and Ripley's
       MASS
LazyData: yes
ByteCompile: yes
License: GPL-2 | GPL-3
URL: http://www.stats.ox.ac.uk/pub/MASS4/
Contact: <MASS@stats.ox.ac.uk>
NeedsCompilation: yes
Packaged: 2024-01-12 08:51:36 UTC; ripley
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb],
       Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port
       ca 1998), Albrecht Gebhardt [trl] (partial port ca
       1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Built: R 4.4.0; x86_64-pc-linux-gnu; 2024-04-24 20:32:09 UTC;
       unix

-- File: /home/lrevilla@irsicaixa.es/.cache/R/renv/sandbox/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu/3df92652/MASS/Meta/package.rds

kevinushey added a commit that referenced this issue Jul 23, 2024
@kevinushey
add fallback check for base / recommended packages (#1948)
c1666ae
@llrs
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llrs commented Jul 24, 2024

As I hope to avoid any more connectivity issues (and I can no longer provide the full message) and the second issue is fixed, I'm closing the issue. Many thanks Kevin for the fast feedback and fixes!

@llrs llrs closed this as completed Jul 24, 2024
@llrs llrs mentioned this issue Jul 24, 2024
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@kevinushey
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Great, I'm glad to hear it!

As far as the curl issues go, you might want to check if there are any environment variable differences in your two sessions; e.g.

system("env | grep CURL")

Perhaps CURL_CA_BUNDLE, or something else, is being set within your regular terminal / R sessions, but not in the sessions where you're using renv for some reason?

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