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! 
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.