I have isolated this hang in my R code to rtracklayer. I see it on my Amazon Linux (AWS) box but not a local server. The AWS box usually, but not always, hangs on either the browserSession() call or the genome(session) call. Here is the strace output of the AWS box:

> library(rtracklayer)
    (...snip library load spam...)
    socket(PF_LOCAL, SOCK_STREAM|SOCK_CLOEXEC|SOCK_NONBLOCK, 0) = 3
    connect(3, {sa_family=AF_LOCAL, sun_path="/var/run/nscd/socket"}, 110) = -1 ENOENT (No such file or directory)
    socket(PF_LOCAL, SOCK_STREAM|SOCK_CLOEXEC|SOCK_NONBLOCK, 0) = 3
    connect(3, {sa_family=AF_LOCAL, sun_path="/var/run/nscd/socket"}, 110) = -1 ENOENT (No such file or directory)
    --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=6982, si_status=0, si_utime=0, si_stime=0} ---

> sessionInfo()
    R version 3.2.2 (2015-08-14)
    Platform: x86_64-redhat-linux-gnu (64-bit)
    Running under: Amazon Linux AMI 2016.03
    
    locale:
    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    [9] LC_ADDRESS=C               LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    
    attached base packages:
    [1] stats4    parallel  stats     graphics  grDevices utils     datasets
    [8] methods   base
    
    other attached packages:
    [1] rtracklayer_1.30.4   GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
    [4] IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1
    
    loaded via a namespace (and not attached):
    [1] XML_3.98-1.4               Rsamtools_1.22.0
    [3] Biostrings_2.38.4          GenomicAlignments_1.6.3
    [5] bitops_1.0-6               futile.options_1.0.0
    [7] zlibbioc_1.16.0            XVector_0.10.0
    [9] futile.logger_1.4.1        lambda.r_1.1.7
    [11] BiocParallel_1.4.3         tools_3.2.2
    [13] Biobase_2.30.0             RCurl_1.95-4.8
    [15] SummarizedExperiment_1.0.2

> session = browserSession()
    socket(PF_INET6, SOCK_DGRAM, IPPROTO_IP) = 3
    socket(PF_INET, SOCK_STREAM, IPPROTO_TCP) = 3
    connect(3, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("128.114.119.133")}, 16) = -1 EINPROGRESS (Operation now in progress)
    getsockopt(3, SOL_SOCKET, SO_ERROR, [0], [4]) = 0
    getpeername(3, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("128.114.119.133")}, [16]) = 0
    getsockname(3, {sa_family=AF_INET, sin_port=htons(34220), sin_addr=inet_addr("10.0.7.56")}, [16]) = 0
    sendto(3, "GET /cgi-bin/hgGateway HTTP/1.1\r"..., 96, MSG_NOSIGNAL, NULL, 0) = 96
    recvfrom(3, "HTTP/1.1 200 OK\r\nDate: Fri, 22 A"..., 16384, 0, NULL, NULL) = 8332
    recvfrom(3, "1000\r\nenu -->\n</div><!-- end mai"..., 16384, 0, NULL, NULL) = 4104
    recvfrom(3, "4000\r\nnatee</OPTION>\n<OPTION VAL"..., 16384, 0, NULL, NULL) = 16384
    recvfrom(3, "ZE=-1>\r\n8e1\r\n25</FONT></TD></TR>"..., 16384, 0, NULL, NULL) = 2293
> genome(session) = "hg19"
    socket(PF_INET, SOCK_STREAM, IPPROTO_TCP) = 4
    connect(4, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("128.114.119.132")}, 16) = -1 EINPROGRESS (Operation now in progress)
    getsockopt(4, SOL_SOCKET, SO_ERROR, [0], [4]) = 0
    getpeername(4, {sa_family=AF_INET, sin_port=htons(80), sin_addr=inet_addr("128.114.119.132")}, [16]) = 0
    getsockname(4, {sa_family=AF_INET, sin_port=htons(52026), sin_addr=inet_addr("10.0.7.56")}, [16]) = 0
    sendto(4, "GET /cgi-bin/hgGateway?db=hg19 H"..., 158, MSG_NOSIGNAL, NULL, 0) = 158
    (...hang indefinitely...)

The strace output of the same code on my local gateway is too long to post here. It never hangs as far as I can tell. Here's the gist: 

Here's the sessionInfo:

> sessionInfo()
    --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=25320, si_status=0, si_utime=0, si_stime=0} ---
    --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=25322, si_status=0, si_utime=0, si_stime=0} ---
    R version 3.2.3 (2015-12-10)
    Platform: x86_64-redhat-linux-gnu (64-bit)
    Running under: CentOS release 6.7 (Final)
  
    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
     [9] LC_ADDRESS=C               LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    
    attached base packages:
    [1] stats4    parallel  stats     graphics  grDevices utils     datasets
    [8] methods   base
    
    other attached packages:
    [1] rtracklayer_1.26.3   GenomicRanges_1.18.4 GenomeInfoDb_1.2.5
    [4] IRanges_2.0.1        S4Vectors_0.4.0      BiocGenerics_0.12.1
    
    loaded via a namespace (and not attached):
     [1] magrittr_1.5            XVector_0.6.0           zlibbioc_1.12.0
     [4] GenomicAlignments_1.2.2 BiocParallel_1.0.3      brew_1.0-6
     [7] foreach_1.4.3           stringr_1.0.0           sendmailR_1.2-1
    [10] tools_3.2.3             fail_1.3                checkmate_1.7.4
    [13] DBI_0.3.1               iterators_1.0.8         BatchJobs_1.6
    [16] digest_0.6.9            base64enc_0.1-3         bitops_1.0-6
    [19] codetools_0.2-14        RCurl_1.95-4.8          RSQLite_1.0.0
    [22] stringi_1.0-1           BBmisc_1.9              backports_1.0.2
    [25] Biostrings_2.34.1       Rsamtools_1.18.3        XML_3.98-1.4

I don't understand how it could be any networking issue with my AWS box. I have no trouble with other internet tasks. I'm hosting a Galaxy server on the box and trying to get Galaxy to run this R script.