rsconnect::deployApp - Unhandled Exception: HTTP 599: Timeout

Using the example I list here (and updating the Bioc pointers to 3.8) I get the same timeout error again relating to mzR that Laurent had last year.

> system.time(deployApp())
Preparing to deploy application...DONE
Uploading bundle for application: 756396...List of 10
 $ name      : chr "jquery"
 $ version   : chr "1.11.3"
 $ src       :List of 1
  ..$ file: chr ""
 $ meta      : NULL
 $ script    : chr "jquery.min.js"
 $ stylesheet: NULL
 $ head      : NULL
 $ attachment: NULL
 $ package   : NULL
 $ all_files : logi TRUE
 - attr(*, "class")= chr "html_dependency"
DONE
Deploying bundle: 1910959 for application: 756396 ...
Waiting for task: 591822017
  building: Parsing manifest
  building: Building image: 1996149
  building: Installing system dependencies
  building: Fetching packages
  building: Building package: mzR
################################ Begin Task Log ################################ 
[2019-03-02T14:59:38.298964259+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 41 not upgraded.
Need to get 67.5 kB of archives.
After this operation, 228 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.10 [67.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.5 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119344 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.10_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.10) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.10) ...
[2019-03-02T14:59:43.427139507+0000] Execute script: packages/build/ncdf4.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libnetcdf-dev netcdf-bin
Reading package lists...
Building dependency tree...
Reading state information...
libnetcdf-dev is already the newest version (1:4.4.0-2).
The following NEW packages will be installed:
  netcdf-bin
0 upgraded, 1 newly installed, 0 to remove and 41 not upgraded.
Need to get 196 kB of archives.
After this operation, 542 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 netcdf-bin amd64 1:4.4.0-2 [196 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 196 kB in 0s (0 B/s)
Selecting previously unselected package netcdf-bin.
(Reading database ... 119366 files and directories currently installed.)
Preparing to unpack .../netcdf-bin_1%3a4.4.0-2_amd64.deb ...
Unpacking netcdf-bin (1:4.4.0-2) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up netcdf-bin (1:4.4.0-2) ...
[2019-03-02T14:59:46.168002041+0000] Execute script: packages/build/igraph.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libglpk-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libamd2.4.1 libbtf1.2.1 libcamd2.4.1 libccolamd2.9.1 libcholmod3.0.6
  libcolamd2.9.1 libcsparse3.1.4 libcxsparse3.1.4 libglpk36 libgmp-dev
  libgmpxx4ldbl libklu1.3.3 libldl2.2.1 libspqr2.0.2 libsuitesparse-dev
  libsuitesparseconfig4.4.6 libumfpack5.7.1
Suggested packages:
  libiodbc2-dev gmp-doc libgmp10-doc libmpfr-dev
The following NEW packages will be installed:
  libamd2.4.1 libbtf1.2.1 libcamd2.4.1 libccolamd2.9.1 libcholmod3.0.6
  libcolamd2.9.1 libcsparse3.1.4 libcxsparse3.1.4 libglpk-dev libglpk36
  libgmp-dev libgmpxx4ldbl libklu1.3.3 libldl2.2.1 libspqr2.0.2
  libsuitesparse-dev libsuitesparseconfig4.4.6 libumfpack5.7.1
0 upgraded, 18 newly installed, 0 to remove and 41 not upgraded.
Need to get 2864 kB of archives.
After this operation, 12.2 MB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libsuitesparseconfig4.4.6 amd64 1:4.4.6-1 [9322 B]
Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libamd2.4.1 amd64 1:4.4.6-1 [21.3 kB]
Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libbtf1.2.1 amd64 1:4.4.6-1 [10.8 kB]
Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcamd2.4.1 amd64 1:4.4.6-1 [20.0 kB]
Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libccolamd2.9.1 amd64 1:4.4.6-1 [21.5 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcolamd2.9.1 amd64 1:4.4.6-1 [15.7 kB]
Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcholmod3.0.6 amd64 1:4.4.6-1 [293 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcsparse3.1.4 amd64 1:4.4.6-1 [26.3 kB]
Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcxsparse3.1.4 amd64 1:4.4.6-1 [62.8 kB]
Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk36 amd64 4.57-1build3 [386 kB]
Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libgmpxx4ldbl amd64 2:6.1.0+dfsg-2 [8948 B]
Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libgmp-dev amd64 2:6.1.0+dfsg-2 [314 kB]
Get:13 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libklu1.3.3 amd64 1:4.4.6-1 [71.5 kB]
Get:14 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libldl2.2.1 amd64 1:4.4.6-1 [10.6 kB]
Get:15 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libumfpack5.7.1 amd64 1:4.4.6-1 [223 kB]
Get:16 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libspqr2.0.2 amd64 1:4.4.6-1 [63.6 kB]
Get:17 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libsuitesparse-dev amd64 1:4.4.6-1 [899 kB]
Get:18 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk-dev amd64 4.57-1build3 [408 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2864 kB in 0s (27.7 MB/s)
Selecting previously unselected package libsuitesparseconfig4.4.6:amd64.
(Reading database ... 119378 files and directories currently installed.)
Preparing to unpack .../libsuitesparseconfig4.4.6_1%3a4.4.6-1_amd64.deb ...
Unpacking libsuitesparseconfig4.4.6:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libamd2.4.1:amd64.
Preparing to unpack .../libamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libbtf1.2.1:amd64.
Preparing to unpack .../libbtf1.2.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libbtf1.2.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcamd2.4.1:amd64.
Preparing to unpack .../libcamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libcamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libccolamd2.9.1:amd64.
Preparing to unpack .../libccolamd2.9.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libccolamd2.9.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcolamd2.9.1:amd64.
Preparing to unpack .../libcolamd2.9.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libcolamd2.9.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcholmod3.0.6:amd64.
Preparing to unp################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 591822025 error: Unhandled Exception: HTTP 599: Timeout during request
Timing stopped at: 50.56 8.041 978.1

Is this from Shiny's side?

Any help would be greatly appreciated! I have several apps I wish to deploy ASAP that rely on mzR. Many thanks in advance! :pray:

Note: I have commented on a similar post relating to this issue.

Here is my sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

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_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] rsconnect_0.8.13     shinythemes_1.1.2    pRoloc_1.23.2       
 [4] BiocParallel_1.16.6  MLInterfaces_1.62.0  cluster_2.0.7-1     
 [7] annotate_1.60.0      XML_3.98-1.17        AnnotationDbi_1.44.0
[10] IRanges_2.16.0       MSnbase_2.8.3        ProtGenerics_1.14.0 
[13] S4Vectors_0.20.1     Biobase_2.42.0       BiocGenerics_0.28.0 
[16] mzR_2.16.1           Rcpp_1.0.0           shiny_1.2.0         

loaded via a namespace (and not attached):
  [1] plyr_1.8.4            igraph_1.2.4         
  [3] lazyeval_0.2.1        splines_3.5.1        
  [5] ggvis_0.4.4           crosstalk_1.0.0      
  [7] ggplot2_3.1.0         digest_0.6.18        
  [9] foreach_1.4.4         htmltools_0.3.6      
 [11] viridis_0.5.1         gdata_2.18.0         
 [13] magrittr_1.5          memoise_1.1.0        
 [15] doParallel_1.0.14     mixtools_1.1.0       
 [17] sfsmisc_1.1-3         limma_3.38.3         
 [19] recipes_0.1.4         gower_0.1.2          
 [21] rda_1.0.2-2.1         dimRed_0.2.2         
 [23] askpass_1.1           lpSolve_5.6.13       
 [25] prettyunits_1.0.2     colorspace_1.4-0     
 [27] blob_1.1.1            xfun_0.5             
 [29] dplyr_0.8.0.1         jsonlite_1.6         
 [31] crayon_1.3.4          RCurl_1.95-4.11      
 [33] hexbin_1.27.2         genefilter_1.64.0    
 [35] impute_1.56.0         DRR_0.0.3            
 [37] survival_2.43-3       iterators_1.0.10     
 [39] glue_1.3.0            gtable_0.2.0         
 [41] ipred_0.9-8           zlibbioc_1.28.0      
 [43] kernlab_0.9-27        prabclus_2.2-7       
 [45] DEoptimR_1.0-8        scales_1.0.0         
 [47] vsn_3.50.0            mvtnorm_1.0-9        
 [49] DBI_1.0.0             viridisLite_0.3.0    
 [51] xtable_1.8-3          progress_1.2.0       
 [53] bit_1.1-14            proxy_0.4-22         
 [55] mclust_5.4.2          preprocessCore_1.44.0
 [57] DT_0.5                lava_1.6.5           
 [59] prodlim_2018.04.18    sampling_2.8         
 [61] htmlwidgets_1.3       httr_1.4.0           
 [63] threejs_0.3.1         FNN_1.1.3            
 [65] RColorBrewer_1.1-2    fpc_2.1-11.1         
 [67] modeltools_0.2-22     pkgconfig_2.0.2      
 [69] flexmix_2.3-15        nnet_7.3-12          
 [71] caret_6.0-81          tidyselect_0.2.5     
 [73] rlang_0.3.1           reshape2_1.4.3       
 [75] later_0.8.0           munsell_0.5.0        
 [77] mlbench_2.1-1         tools_3.5.1          
 [79] LaplacesDemon_16.1.1  generics_0.0.2       
 [81] RSQLite_2.1.1         pls_2.7-0            
 [83] evaluate_0.13         stringr_1.4.0        
 [85] mzID_1.20.1           yaml_2.2.0           
 [87] ModelMetrics_1.2.2    knitr_1.21           
 [89] bit64_0.9-7           robustbase_0.93-3    
 [91] randomForest_4.6-14   purrr_0.3.0          
 [93] packrat_0.5.0         dendextend_1.9.0     
 [95] ncdf4_1.16            nlme_3.1-137         
 [97] whisker_0.3-2         mime_0.6             
 [99] biomaRt_2.38.0        compiler_3.5.1       
[101] rstudioapi_0.9.0      e1071_1.7-0.1        
[103] affyio_1.52.0         tibble_2.0.1         
[105] stringi_1.3.1         highr_0.7            
[107] lattice_0.20-38       trimcluster_0.1-2.1  
[109] Matrix_1.2-15         markdown_0.9         
[111] gbm_2.1.5             pillar_1.3.1         
[113] BiocManager_1.30.4    MALDIquant_1.18      
[115] data.table_1.12.0     bitops_1.0-6         
[117] httpuv_1.4.5.1        R6_2.4.0             
[119] pcaMethods_1.74.0     affy_1.60.0          
[121] hwriter_1.3.2         promises_1.0.1       
[123] gridExtra_2.3         codetools_0.2-16     
[125] MASS_7.3-51.1         gtools_3.8.1         
[127] assertthat_0.2.0      CVST_0.2-2           
[129] openssl_1.2.2         withr_2.1.2          
[131] diptest_0.75-7        hms_0.4.2            
[133] grid_3.5.1            rpart_4.1-13         
[135] timeDate_3043.102     coda_0.19-2          
[137] class_7.3-15          rmarkdown_1.11       
[139] segmented_0.5-3.0     lubridate_1.7.4      
[141] base64enc_0.1-3    

FYI - also updated to latest stable R release on another machine and got the same error.